The latest offering from the Laika animation studio doesn’t have the warmth of “ParaNorman” or the quirkily dark charm of “Coraline,” but though it’s not quite their equal, “The Boxtrolls” offers considerable pleasures of its own. Loosely based on Alan Snow’s children’s book “Here Be Monsters!,” it emerges as a weird reworking of the Pied Piper story with no rats but so much cheese you half expect to see Wallace and Gromit make an appearance. And though it’s more than a mite chilly emotionally, it compensates with some understated British wit and a typically good moral about not judging books by their covers—or in this case trolls by the cardboard boxes they wear.

The titular critters are actually a peace-loving bunch that venture out at night to go through the debris left behind by the human inhabitants of Cheesebridge and cart bits and pieces back to their subterranean cave, using them to build their communal space or merely keeping them as souvenirs. But they’ve been made terrifying to the residents above because of a rumor that they abducted the son of the town’s most productive inventor Herbert Trubshaw (Simon Pegg), who disappeared along with the boy, and have designs on the rest of the burg’s children. The misplaced fear of the creatures has been fed by snarling Archibald Snatcher (voiced by Ben Kingsley) to extract a pledge from dotty Lord Portley-Rind (Jared Harris), the leader of the town’s white-hat-wearing aristocrats who spend their days sniffing and sampling the finest of cheeses: if Snatcher clears Cheesebridge of the trolls, he’ll be rewarded with a white hat of his own, and entrance into the prestigious inner sanctum of the tasting-room.

So Snatcher has assembled a group of minions—led by Mr. Trout (Nick Frost) and Mr. Pickle (Richard Ayoade)—to capture all the boxtrolls during their nighttime excursions above ground. Their work is proceeding nicely until a boy the trolls adopted—called Eggs from the box he wears and voiced by Isaac Hempstead Wright—falls in with Lord Portly-Rind’s self-confident daughter Winnifred (Elle Fanning) to save the critters and keep Snatcher from taking control of the town. The actual identity of Eggs, and of the crazed prisoner Snatcher keeps locked up in a deep dungeon, will come as no surprise; nor will the outcome of the final confrontation in which Snatcher demands his promised compensation from Winnifred’s father as he sits atop a huge belching machine with a hostage dangling from its claw-like appendage.

The stop-motion animation of “The Boxtrolls,” complemented by the 3D format, is almost willful in its avoidance of cuteness in the physical portrayal of its characters. That’s to be expected of Snatcher, who’s depicted as a Dickensian villain ratcheted up several levels. (In another veddy British touch, he appears at one point as Madame Frou Frou, one of the town’s most beloved hags, and looks even worse in drag.) But it’s more unusual in the case of the trolls, who have none of the smoothly likable look of Shrek, and of Eggs, a gawky lad with a twisty mouth, and Winnifred, whose angular face isn’t all that inviting. Even the backgrounds have a distinctly unlovely look to them—not only the interior of Snatcher’s factory and the trolls’ underground lair but the dank streets of Cheesebridge. Frankly the semi-grotesquerie might frighten some smaller children, particularly in the scenes when Snatcher, determined to prepare himself for his ascent to the role of white hat despite a terrible allergic reaction to cheese, bursts out in hideously bulbous pustules. (On the other hand, kids nowadays seem to enjoy this sort of stuff, so maybe they’ll be clapping in glee as their parents turn away.)

But the distinctive look of the movie complements its equally unusual tone, which opts only infrequently for belly-laughs and instead courts amused giggles from the wry witticisms voiced almost sotto-voce by the likes of Frost and Ayoade. Kingsley of course shouts to the rafters as Snatcher (and brings a nice falsetto whine to Frou-Frou), but Harris is far more restrained, oozing absurd hauteur as the dreamily dim-witted Portly-Rind. Youngsters Wright and Fanning are agreeable enough, especially in the party scene in which she attempts to introduce the lad to proper human society, but one must wonder at the waste of Toni Collette, who’s stuck in what amounts to little more than a cameo as Lady Portly-Rind.

“The Boxtrolls” demonstrates that Laika refuses to get stuck in a rut even if, like its two predecessors, it’s centered on children who serve to bridge the gap between the human world and another which it fears. Its very British blend of humor and horror might not go down well with American audiences who are used to something more generically comic. But animation connoisseurs will doubtlessly take to it as enthusiastically as they did the earlier films. And they should definitely stay through the closing credits, which feature some of the script’s cleverest moments, including a delicious final gag that blends in a brief glimpse of the “real” world.