Farmland is the important soil carbon pool of terrestrial ecosystems and organic nutrient pool for crop growth. To clarify the impact of climate warming on the soil carbon pool, this study analyzed the effects of warming and fertilization on soil organic carbon and its labile components under rice-wheat rotation using a free-air temperature increase system. The variation in soil carbon pool management index (CPMI) was also evaluated. The results showed that the combined effects of warming and fertilization on soil organic carbon content and labile organic carbon components were insignificant. Warming increased the soil organic carbon (SOC) content, and the differences between warming and the ambient control in total organic carbon (TOC) and recalcitrant organic carbon (ROC) reached a statistically significant level. Compared with those under the ambient control, the contents of TOC, ROC, and labile organic carbon (LOC) subjected to warming increased by 7.72%, 7.42%, and 10.11%, respectively. The increased microbial biomass carbon (MBC) content (20.4%) and decreased particulate organic carbon (POC) content (36.51%) may have been the main reason for the variation in SOC. Warming showed no significant effect on soil dissolved organic carbon (DOC) content, whereas it markedly reduced its soluble microbial by-product components (41.89%). The results also showed that fertilization had no significant effect on soil TOC, ROC, and LOC, but it notably reduced the contents of DOC and POC and increased the MBC content. Compared with those under the control without fertilization, the contents of DOC and POC subjected to fertilization decreased by 35.44% and 28.33%, respectively, and the MBC content increased by 33.38%. Additionally, fertilization tended to increase the anthropogenic humus component (5.13%) and soluble microbial by-product component (29.41%) in dissolved organic matter and reduce the terrestrial humus component (13.33%). Warming and fertilization both tended to improve soil CPMI. Affected by SOC and LOC, the increase in soil carbon pool index and soil lability index were the main reason for the increase in soil CPMI under warming and fertilization, respectively. Overall, the results revealed that climate warming can affect the soil carbon pool by changing soil labile carbon components, which are not affected by fertilization.