The mechanism of the effects of different fertilizer types on soil organic carbon (SOC) content and crop yield under different climate conditions is still unclear. We conducted a meta-analysis to evaluate the impacts of different fertilizer types (CK, no fertilizer; F, inorganic fertilizer; S, organic fertilizer; and FS, inorganic combined with organic fertilizer) on SOC content and crop yield in China. Overall, compared with the CK treatment, fertilizer significantly (p < 0.05) increased the SOC content in the 0–20 cm soil depth by 21.5%. In addition, the fertilizer treatments significantly increased the SOC content regardless of the air temperature, and the magnitude of the increase in the SOC content under the fertilizer treatments was lowest at a mean annual temperature of < 10 °C, which was significantly less than that at 10–15 °C. Moreover, fertilizer, especially the FS treatment, significantly improved the crop yield by 119.7%. The magnitude of the increase in crop yield was highest for the experimental duration of 5–15 years under the F and S treatments. Our results suggest that the long-term application of inorganic combined with organic fertilizer may be an appropriate fertilizer treatment for the development of sustainable agriculture by improving SOC content and crop production.