Research on the effect of long-term warming on rice in cool region is still rare. This study used the widely cultivated japonica rice Jiyang100 in Northeast China as the experiment material. We set up warming treatments at three growth stages of rice in the field: the tillering-panicle initiation stage (T1), the whole growth stage (T2) and the grain-filling stage (T3). The rice yield showed a trend of T1 > T2 > T3 > CK in both years. The positive effects of T1, T2 and T3 on the total number of spikelets per hole significantly increased the yield, with average increased by 11.5%, 9.9% and 6.5%, respectively. Each warming treatment had significant positive effect on the stay-green traits, photosynthesis, sucrose synthesis, and nitrogen metabolism of rice. The yield was significantly positively correlated with SPAD, soluble sugar content, sucrose content, SPS, NR, GS, and GOGAT activity. The physiological models constructed by SPAD and sucrose content could explain the changes of the yield (R2=0.704). The stay-green traits had significant correlation between carbon and nitrogen metabolism, and it played a pivotal role in them. Wherein, SPAD had significant positive correlation with soluble sugar content, soluble protein content, NR, GS, GOGAT and GDH activity, and significant negative correlation with AI activity. The stay-green ability had significant positive correlation with Pn, soluble sugar content and soluble protein content. The above results indicated that the coupling interaction of stay-green traits, nitrogen metabolism and carbon metabolism increased the sink capacity potential and sink storage supply capacity, which was the reason for the increase in rice yield under long-term warming in cool region.