Starch retrogradation is of great importance to the quality of starch-based food. This study investigated the effect of partial gelatinization (PG) synergizing with polyphenol (epicatechin, EC; epigallocatechin gallate, EGCG) on the multi-scale structure and short/long-term retrogradation of corn starch (CS). The PG synergizing with EC/EGCG substantially suppressed the short/long-term retrogradation properties of CS. These could be confirmed by the decreased storage modulus and viscosity, the relative crystallinity (1.54%, 3.56%), and the retrogradation degree (9.99%, 20.18%) of CS during storage for 1, 14 days after PG synergizing with EGCG and EC, respectively. This is because PG treatment promoted the hydrogen bond interaction between disordered starch molecules and EC/EGCG. These were proven by the larger aggregation, more and brighter fluorescents, and the reduced long/short-range order structures in CS after PG synergizing with EC/EGCG. This study is helpful for the development of foods with enhanced nutrition and low-retrogradation.