This study comprehensively investigated the effect of germination on the physicochemical properties and molecular structure of japonica brown rice varieties. During germination, the amylose content of the rice reduced by 1.1–4.27 g/100g, while the amylopectin content reduced by at least 9.52%. Germination increased the reducing sugar content, and α-amylase activity of japonica brown rice and upregulated the expression of α-amylase-encoding genes. Furthermore, germination disrupted the short-range ordered structure of brown rice flour and reduced its relative crystallinity. In contrast, it had little effect on the A-type crystal structure of brown rice starch. Notably, germination enhanced thermal stability and reduced retrogradation in japonica brown rice. Principal component analysis revealed that the gene regulation was positively correlated with α-amylase activity, which in turn influenced the hardness, thermal stability, and retrogradation properties of brown rice. This study provides data supporting the optimization of japonica and the development of germinated grain foods.