The processing quality of indica rice must undergo ripening after harvest to achieve stability and improvement. However, the mechanism underlying this process remains incompletely elucidated. Starch, the predominant component in indica rice, plays a crucial role in determining its properties. This study focused on analyzing the rheological properties and starch fine structure, as well as the related biosynthetic enzymes of indica rice during the after-ripening process. The results showed that after-ripened rice exhibited increased elastic modulus (G′) and viscous modulus (G″), accompanied by a decrease in the loss tangent (Tan δ), indicating an enhancement in viscoelasticity and the gel network structure. Moreover, the proportions of amylopectin super long chains (DP 37–60) decreased, while those of medium chains (DP 13–24 and DP 25–36) or short chains (DP 6–12) of amylopectin increased. Additionally, the activities of starch branching enzyme (SBE) and starch debranching enzyme (DBE) declined over the after-ripening period. Pearson correlation analysis revealed that the rheological properties of after-ripened rice were correlated with the chain length distribution (CLD) of starch, which, in turn, was associated with its related endogenous enzymes. These findings provied new insights into understanding the quality changes of after-ripened indica rice. Display omitted •The elastic modulus and viscous modulus of rice increased during after-ripening.•The chain length distribution of amylopectin undergoed changes during after-ripening.•The activities of starch branching enzyme and starch branching enzyme decreased during after-ripening.•The starch biosynthesis enzymes changed the starch structure and thus affected the rheological properties of rice.