The study investigated the impact of pea protein isolate (PPI) on the short-term and long-term retrogradation behavior of pea starch (PS). Dynamic time scanning and water migration analysis revealed that the presence of PPI enhanced water mobility within the PS gel during short-term storage (4 °C, 8 h) and impeded amylose gelation, effectively suppressing the short-term retrogradation of amylose. Over long-term storage (4 °C, 14 d), PPI reduced the retrogradation enthalpy and the ordered structure of starch molecules. The relative crystallinity and retrogradation degree reduced by 40.6% and 29.9%, respectively, as the PPI content increased from 0 to 12%. Textural profile analysis showed PPI decreased the gel hardness and induced the formation of a weak gel of PS, thereby delaying the long-term retrogradation of amylopectin. Scanning electron microscopy analysis further confirmed that the PS-PPI mixed gel exhibited a more disordered and loose structure compared to the PS gel, which resulted from PPI inhibiting the rearrangement and aggregation of amylose and amylopectin molecules. These findings suggested that PPI exhibited the potential to inhibit the short-term and long-term retrogradation of PS, thus providing valuable theoretical evidence for enhancing the development and research of pea-based products.