Fertilizations affect soil organic carbon (SOC) content but the relative influences of the edaphic and climate factors on SOC storage are rarely studied across wide spatiotemporal scales. This study synthesized long-term datasets of fertilization experiments in six typical Chinese croplands, and calculated annual C input from crops and manure amendments, changes in SOC storage (ΔSOC) and C sequestration efficiency (i.e. the percentage of soil C change per unit of C input, hereafter referred as CSE) in 0-20 cm soil over three decades. Three fertilization treatments include no fertilization (CK), chemical nitrogen, phosphorus and potassium fertilizers (NPK) and combined chemical fertilizers and manure (NPKM). Results showed significant fertilization effects on C input and ΔSOC (NPKM>NPK>CK), and significantly higher CSE in Qiyang at Hunan than Zhengzhou at Henan and Heihe at Heilongjiang. The variance partitioning analysis (VPA) showed more variance of CSE can be explained by edaphic factors (up to 39.7%) than other factors. Furthermore, soil available N content and pH were identified as the major soil properties explaining CSE variance. This study demonstrated key controls of soil fertility factors on SOC sequestration and informs the need to develop strategic soil management plan to promote soil carbon sequestration under long-term intensive fertilization.