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Understanding nacre’s bottom-up biomineralization mechanism, particularly, how individual aragonite platelets are formed, has long remained elusive due to its crystallographic peculiarity and structural complexity. Here we report that crystallographic order-disorder transition can be triggered within individual aragonite platelets in pristine nacre by means of heat treatment and/or inelastic deformation, offering a unique opportunity to discriminate mysterious aragonite nanoparticles in transmission electron microscopy. Our findings unambiguously uncover why aragonite nanoparticles in pristine nacre have long been inaccessible under TEM observation, which is attributed to the monocrystal-polycrystal duality of the aragonite platelet. The underlying physical mechanism for why an individual aragonite platelet adopts a highly oriented attachment of aragonite nanoparticles as its crystallization pathway is, for the first time, explained in terms of the thermodynamics. The finding of an order-disorder transition in nacre provides a new perspective for understanding the formation for other biominerals.