Grain size is a crucial determinant of rice yield, yet the molecular mechanisms controlling this trait remain only partially understood. Here, we identified the JMJ720 locus as a key regulator of grain size through map-based cloning. The jmj720 mutant was found to exhibit significantly larger grains when compared to the wild type (WT). JMJ720 encodes a protein with a Jumonji C (JmjC) domain that serves as a histone H3K9me2 demethylase. In this study, we found that JMJ720 decreases the methylation level of H3K9me2 at the OsNDB2 locus, which codes for a putative rotenone-insensitive type II NAD(P)H dehydrogenase, thereby promoting OsNDB2 expression. Elevated expression of OsNDB2 was associated with reduced grain size, whereas increased H3K9me2 methylation at the OsNDB2 locus in the jmj720 mutant led to the repression of its expression, resulting in larger grain size. These findings unveil a novel epigenetic mechanism by which a JmjC-domain protein regulates grain size and offer a potential strategy for breeding rice varieties with enhanced grain size and yield.