The combined application of organic manure and chemical fertilizers is an effective way to enhance soil organic carbon (SOC) sequestration through its influences on organic carbon (OC) input and the stability of SOC fractions. However, there is limited information on the carbon sequestration efficiency (CSE) of chemically separated SOC fractions and its response to OC input under long-term fertilization regimes, especially at different sites. This study used three long-term fertilization experiments in Gongzhuling, Zhengzhou and Qiyang spanning 20 years to compare the stocks and CSE in four different OC fractions (very labile OC, labile OC, less labile OC, and non-labile OC) and their relationships with annual OC input. Three treatments of no fertilization (CK), chemical nitrogen, phosphorous, and potassium fertilizers (NPK), and chemical NPK combined with manure (NPKM) were employed. The results showed that compared with CK, NPKM resulted in enhanced SOC stocks and sequestration rates as well as CSE levels of all fractions irrespective of experimental site. Specifically for the very labile and non-labile OC fractions, NPKM significantly increased the SOC stocks by 43 and 83%, 77 and 86%, and 73 and 82% in Gongzhuling, Qiyang, and Zhengzhou relative to CK, respectively. However, the greatest changes in SOC stock relative to the initial value were associated with non-labile OC fractions in Gongzhuling, Zhengzhou, and Qiyang, which reached 6.65, 7.16, and 7.35 Mg ha^-1 under NPKM. Similarly, the highest CSE was noted for non-labile OC fractions under NPKM followed sequentially by the very labile OC, labile OC, and less-labile OC fractions, however a CSE of 8.56% in the non-labile OC fraction for Gongzhuling was higher than the values of 6.10 and 4.61% in Zhengzhou and Qiyang, respectively. In addition, the CSE for the passive pool (very labile+labile OC fractions) was higher than the active pool (less-labile+non-labile OC fractions), with the highest value in Gongzhuling. The redundancy analysis revealed that the CSEs of fractions and pools were negatively influenced by annual OC input, mean annual precipitation and temperature, but positively influenced by the initial SOC and total nitrogen contents. This suggests that differential stability of sequestered OC is further governed by indigenous site characteristics and variable amounts of annual OC input.