The search for a method to control structural transformations of layered coordination polymers is highly desirable to modulate their properties and functions. Herein, we report the construction of a novel coordination polymer named ZnC16 with Zn(II) ions coordinated to isophthalate ligands bearing an n-hexadecyloxy chain (C162-). Its structure consists of a layer-by-layer structure of a rigid two-dimensional coordination network and an assembly of alkyl chains as a thermally responsive moiety. Single crystals of ZnC16 exhibit a thermal crystal-to-crystal phase transition behaviour dominated by disordering/ordering of alkyl chains, which induces the expansion and shrinkage of the distance within the rigid 2D coordination networks. Microscopic observation revealed that the thermal phase transition of ZnC16 induces a significant change in their crystal morphology: a reversible macroscopic elongation/shrinkage of crystal dimensions driven by the displacement of interlayer distances and an irreversible delamination and polycrystal slippage driven by constraints generated from this phase transition. Our result provides a new direction to modulate the dynamic behaviour and related properties and functions of layered coordination polymers where the thermally responsive character of flexible alkyl chains plays an important role in tuning interlayer interactions.