Rice readily undergoes yellowing under heat stress. Traditionally viewed as a sign of quality decline, this phenomenon is concurrent with the accumulation of flavonoids. Consequently, our study optimized flavonoid extraction (60-min ultrasound, 40-min shaking time, 50 g/mL solid-liquid ratio) and analyzed yellowing-stage dynamics. Total flavonoids increased with yellowing, correlating with enhanced antioxidant, antibacterial (minimum inhibitory concentration: 6.25 mg/mL for E. coli, 5 mg/mL for S. aureus), and hypoglycemic activities. Metabolomics identified four principal flavonoid subclasses (flavones, flavonols, isoflavones, and anthocyanidins) exhibiting differential accumulation patterns. Flavonols and flavones predominated in Mudanjiang japonica, while isoflavones showed maximal impact in Xiangwanxian indica. Luteolin, diosmetin, 6-methoxyaromadendrin 3-O-acetate, pelargonidin, syringetin, laricitrin, and 2'-O-methylisoliquiritigenin drove Mudanjiang japonica's yellowing. Xiangwanxian indica exhibited thermal sensitivity through rapid qualitative flavonoid changes rather than quantitative increases, causing pronounced yellowing. These findings provide novel insights into the mechanisms of rice yellowing and a theoretical framework for potential applications of yellowed rice.