According to the difference in the degree of difficulty or easiness of decomposition, the soil organic carbon can be divided into readily oxidizable organic carbon and hardly oxidizable organic carbon. The readily oxidizable organic carbon plays an important role in supplying ability of soil nutrient, while hardly oxidizable organic carbon contributes to stabilizing the soil structure, and it is related to the storage of soil organic carbon. Meanwhile, soil carbon pool management index (CPMI) can reflect the effects of external condition on soil organic carbon contents and active organic carbon contents, and comprehensively reflect the extent of decline or update of soil quality. However, there is little information on the effect of chicken manure co-applied with inorganic fertilizer on soil organic carbon oxidation stability and CPMI, especially the study of kidney bean/maize rotation soil was scarcely reported. Therefore, for exploring the effect of chicken manure co-applied with nitrogen fertilizer in different proportions on soil organic carbon oxidation stability and CPMI in kidney bean/maize rotation soil, a field experiment, including four treatments, i.e., N100 (100% of nitrogen was provided by urea), M10N90 (10% and 90% of nitrogen was provided by chicken manure and urea, respectively), M30N70 (30% and 70% of nitrogen was provided by chicken manure and urea, respectively), and M50N50 (50% and 50% of nitrogen was provided by chicken manure and urea, respectively) were carried out. The aim was to determine the effects of different treatments on total organic carbon (TOC), microbial biomass carbon (MBC), readily oxidizable carbon (ROC) contents, organic carbon oxidation stability, as well as CPMI of kidney bean/maize rotation soil during the 2009—2014 period. Results indicated that the TOC contents of M10N90, M30N70 and M50N50 treatments were increased by 5.21%, 12.74% and 19.87% in comparison with the N100 treatment, respectively. The MBC and ROC contents and CPMI achieved the highest value in M30N70 treatment and had significant differences with other treatments, which showed 54.03%, 16.50% and 10.43% increases in ROC content and 75.10, 30.75 and 27.94 increases in CPMI, respectively, compared with those in treatments of N100, M10N90 and M50N50. However, the oxidation stability index of organic carbon in M30N70 treatment was obviously lower than other treatments, which was reduced by 35.95% compared with N100 treatment. Furthermore, the M30N70 treatment could significantly increase yield and improve quality of kidney bean, which had statistically significant differences with other treatments. Correlation analysis revealed that yield and Vc content of kidney bean were significantly or extremely significantly correlated with microbial biomass carbon, readily oxidizable carbon, organic carbon oxidation stability and carbon pool management index in the soil, indicating close inner link among each indicator. In conclusion, the application of chicken manure co-applied with inorganic fertilizer, especially the M30N70 treatment, was beneficial to soil quality amelioration and soil nutrient-supply capacity improvement as well as growth of high-yield and high-quality kidney bean in the rotation plantation.