Salt-alkaline stress generally leads to soil compaction and fertility decline. It also restricts rice growth and nutrient acquisition, so reduces rice yield. However, little is known about the effect of salt-alkaline stress on the carbon and nitrogen metabolism of rice. In this study, two relatively salt-alkaline tolerant (Changbai 9 and Dongdao 12) and sensitive (Jinongda 138 and Tongyu 315) rice cultivars were grown in a field experiment conducted with two soil types including black soil and salt-alkaline soil to evaluate the characteristics of yield, carbon and nitrogen metabolism in rice. Results showed that yield and nitrogen use efficiency (NUE) in rice greatly decreased under salt-alkaline stress. Changbai 9 (CB9) and Dongdao 12 (DD12) showed higher NUE than Jinongda 138 (JND138) and Tongyu 315 (TY315) under the salt-alkaline stress. Additionally, carbon and nitrogen metabolism enzyme activity and compound content were significantly affected by salt-alkali stress; different performances were observed between cultivars under salt-alkaline stress. In conclusion, our results indicate that salt-alkaline tolerant rice cultivars may have more stable carbon and nitrogen metabolism than sensitive genotypes under salt-alkaline conditions.