Although the role of OsHY5L2 in promoting photomorphogenic development is well characterized, its function in regulating rice quality is poorly understood. In this study, we found that OsHY5L2 plays an important role in regulating starch metabolism and modulating its fine structure and physicochemical properties. Overexpression of OsHY5L2 significantly reduced the chalky grain rate and degree of chalkiness but dramatically increased the head rice rate. OsHY5L2 was found to negatively regulate the accumulation of starch in rice endosperm by inhibiting starch biosynthesis and promoting starch hydrolysis. Transcriptomic analysis revealed that OsHY5L2 mainly regulated the expression of genes encoding enzymes involved in starch and sucrose metabolism. Moreover, OsHY5L2 overexpression induced the formation of numerous pinhole structures on the surfaces of starch granules. Analysis of the amylopectin chain length distribution showed that overexpression of OsHY5L2 decreased the proportion of ultra-short chains (DP 6–7) and intermediate chains (DP 13–24) of amylopectin while increasing the proportion of short chains (DP 8–12) and long chains (DP 25–36). Further studies demonstrate that OsHY5L2 overexpression altered the pasting properties of rice starch by affecting its multi-level structure and function. The results of this study improve our understanding of the functions of OsHY5L2 in regulating rice quality.