Although the contribution of calcium ion (Ca2+) to stabilizing organic carbon (OC) in soils has been known for years, we still have a limited understanding of the quantity and molecular composition of Ca2+ bound SOC (Ca-OC) evolution in response to long-term fertilization. Here we report the role of Ca2+ in the accumulation of OC in the topsoil (0–20 cm) from two long-term (25–37 years) fertilization experiment sites. Approximately 4.54–19.27% and 9.00–25.15% of SOC was bound with Ca2+ in the Ferric Acrisol and Fluvic Cambisol, respectively. The application of NPK mineral fertilizers (NPK) decreased (p < 0.05) the Ca-OC stocks from 3.40 t ha−1 to 0.96 t ha−1 and from 2.03 t ha−1 to 1.17 t ha−1 in the Ferric Acrisol and Fluvic Cambisol, respectively. Swine manure (M) addition did not change (p > 0.05) the Ca-OC stock in Ferric Acrisol, but enhanced (p < 0.05) that from 2.03 t ha−1 to 9.75 t ha−1 in Fluvic Cambisol. Fourier transform infrared and carbon (1s)-near X-ray absorption spectroscopies showed that Ca2+ was mainly bound with aromatic carbon and carboxylic carbon. Long-term M fertilization facilitated the binding of Ca2+ with O-alkyl C, suggesting an increment of Ca-linked polysaccharide. Calcium ion was preferentially associated with 13C enriched organic matter (OM). Mineral fertilization promoted the 13C-enriched organic compounds in the Ca-OC, while organic fertilization facilitated the binding of 13C-depleted organic C with Ca2+. This study suggests that Ca-OC may be a potentially vital and stable OC pool in arable soils, and provides direct evidence for the preferential association of OC with Ca2+ in edaphic environments.