The rapid advancement of technology has positioned devices based on two-dimensional materials as a key solution to overcoming the limitations of traditional semiconductor materials. Among these, the ferroelectric compound CuInP2S6 (CIPS) has attracted significant attention for its multiple ferroelectric polarization states. However, its structural complexity, particularly its susceptibility to copper deficiency, presents notable challenges for further research. This study investigates copper-deficient CIPS (Cu: CIPS) to explore the structure–property relationship between ferroelectricity and structural composition at macroscopic and microscopic levels. Using spherical aberration-corrected scanning transmission electron microscopy, copper deficiency is shown to induce phase separation in CIPS, resulting in the coexistence of CIPS (Cc), CIPS (Cc′) (where the two layers experience a sliding displacement of 1/6b along the b-axis) and an In4/3P2S6 structure containing small amounts of Cu (Cu: IPS) structure. Moreover, the intermediate phase exhibits a lack of ferroelectric switching response in piezoelectric force microscopy measurements. This work elucidates the microstructural evolution of Cu: CIPS, identifies the mechanism underlying the failure of ferroelectric switching in CIPS, and provides valuable insights for advancing CIPS-based ferroelectric memory devices.