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Here, biomimetic organic nanocrystals with a butterfly-like morphology (BM) were first constructed from a windmill-like bulky small molecule, T(DAF)3. The BMs possess a peculiar “Janus” feature with a butterfly-shaped front side and cross-veined back side. Evolution observations clearly reveal that this unusual 3D architecture is originated from the preferential growth of {011} and {0–11} crystal faces of a core. Additionally, the BMs are pH-sensitive and can be converted reversibly with a cube-shaped morphology (CM). Detailed microscopic observations in combination with systematically single-crystal determinations suggest that the BMs and CMs are polymorphs and the acid/base responsive conformational conversion of T(DAF)3 is responsible for the polymorphic transformation. Finally, the effect of molecular-level conformation on packing and morphology is demonstrated. The nonplanar 3D configuration, flexible conformational transitions, and variable supramolecular interactions of T(DAF)3 are regarded as the crucial factors for the realization of the biomimetic morphology and polymorphic transformation of organic microcrystals. The rotational isomerism-morphology relationship of organic small molecules can serve as a model, providing a guideline for complex micro/nanocrystals of organic systems for optoelectronic or bionic applications.