There is great uncertainty in the responses of soil organic carbon (C) to climate warming in the saline-alkali grassland in northern China. In this study, we explored the responses of soil organic C and nitrogen (N) fractions in different soil layers to the manipulative warming using a 5-year continuous warming experiment in a saline-alkali grassland of Youyu, Shanxi Province. The experiment with a randomized block design had been conducted since 2017 at the Youyu Loess Plateau Grassland Ecosystem Research Station of Shanxi Agricultural University, where open-top air chambers (OTCs) were established to simulate climate warming. Our results showed that warming treatments did not significantly affect soil organic C, total N, particulate organic C (POM-C) and N (POM-N), Mineral-associated organic C (MAOM-C) and N (MAOM-N), dissolved organic C (DOC) and N (DON) and microbial biomass C (MBC) and N (MBN) fractions. Moreover, the ratio between soil C and N fractions, with the exception of MAOM-C/MBC which decreased owing to warming treatments, did not significantly change with warming treatments. However, we found that soil depth had a significant effect on soil organic C and N fractions, except for DOC and MBC, where soil C and N fractions showed a decreasing trend with soil depth. In contrast, the ratio between soil C and N fractions, except for MAOM-N/N and MBC/C, increased with soil depth. Warming and soil depth interactively affected POM-N/MBN and MAOM-N/MBN, suggesting a discrepancy between MBN and POM-N or MAOM-N from different soil layers in response to warming. Shifts in the ratio of N fractions of different soil layers under warming treatment may be attributable to shifts in the grass abundance, forb abundance, litter mass, soil pH and soil moisture. Among them, litter mass and soil pH pronouncedly associated with POM-N/MBN and MAOM-N/MBN, grass abundance and forb abundance significantly related to POM-N/N, and soil physicochemical properties such as soil pH and soil moisture correlated with MAOM-N/N. Overall, the results as mentioned above highlight the adaptation of soil organic C and N fractions to short-term climate warming in the saline-alkali grassland. In addition, the ratio of N fractions in different soil layers showed a stronger response to warming treatment compared to soil C fractions. These findings could improve our understanding for the patterns of soil organic C pool in response to climate warming in the saline-alkali grassland, and provide support for the conservation and restoration of fragile grassland ecosystems in northern China.