Under the assistance of the state‐of‐the‐art meta‐dynamics simulations, in this contribution, we report a push‐pull‐type acylhydrazone 4(Z) ([Z)‐2‐(naphthalen‐2‐yloxy)‐N'‐(pyridine‐2‐ylmethylene)acetohydrazide] connecting an electron‐donating naphthalene ether group with an accepting pyridyl unit, which could be thermally converted to its configurational isomer 4(E) ([E)‐2‐(naphthalen‐2‐yloxy)‐N'‐(pyridine‐2‐ylmethylene)acetohydrazide]. The thermally triggered Z‐to‐E configurational isomerization not only involves up to five chemical bonds undergoing 180° rotation in the backbone of acylhydrazone, but changes the crystal packing symmetry from a centrosymmetric space group to a non‐centrosymmetric one. Most impressively, the acentric crystal arrangement of 4(E) exhibits a second‐harmonic generation (SHG) active response, about 2.5 times than that of KH2PO4 (KDP) standard.