Cropland soil organic carbon (SOC) is undergoing substantial alterations due to both environmental and anthropogenic changes. Although numerous case studies have been conducted, there remains a lack of quantification of the consequences of such environmental and anthropogenic changes on the SOC sequestration across global agricultural systems. Here, we conducted a global meta-analysis of SOC changes under different fertilizer managements, namely unbalanced application of chemical fertilizers (UCF), balanced application of chemical fertilizers (CF), chemical fertilizers with straw application (CFS), and chemical fertilizers with manure application (CFM). We show that topsoil organic carbon (C) increased by 0.9 (0.7–1.0, 95% confidence interval (CI)) g kg−1 (10.0%, relative change, hereafter the same), 1.7 (1.2–2.3) g kg−1 (15.4%), 2.0 (1.9–2.2) g kg−1 (19.5%) and 3.5 (3.2–3.8) g kg−1 (36.2%) under UCF, CF, CFS and CFM, respectively. The C sequestration durations were estimated as 28–73 years under CFS and 26–117 years under CFM but with high variability across climatic regions. At least 2.0 Mg ha−1 yr−1 C input is needed to maintain the SOC in ~85% cases. We highlight a great C sequestration potential of applying CF, and adopting CFS and CFM is highly important for either improving or maintaining current SOC stocks across all agro–ecosystems.