Abstract: Nutrient recycling plays an important role in soil nutrient conservation and is an effective measure for fertilizing soils in agro-ecosystems. This study relied on a long-term experiment (since 2001) on an agricultural management system conducted by the Luancheng Agroecosystem Experimental Station of the Chinese Academy of Sciences. The aim of this study was to provide a theoretical basis for developing agricultural management measures for soil fertility cultivation and enhancing soil carbon sequestration potential. Four treatments were set: no fertilization (i.e., conventional, CK), all applications of chemical fertilizer (NPK), chemical fertilizer and 80% of the above-ground output feeding pigs through belly (as pig manure) to the field (MNPK), and chemical fertilizer and straw crushed direct return to the field (SNPK). The soil organic matter (SOM), total nitrogen (TN), available phosphorus content (AP), and composition of soil carbon and nitrogen pools of the treatments were determined. The results showed that the implementation of nutrient recycling significantly increased the contents of SOM, TN, and AP in the soil in the order of MNPK > SNPK > NPK > CK. After 18 years, we found that SOC, TN, and AP storage in the 0–20 cm soil layer increased in MNPK by 9.21 t(C)∙hm⁻², 1.01 t(N)∙hm⁻², and 144.87 t(P)∙hm⁻², respectively. The SOC, TN, and AP storage in SNPK increased by 4.51 t(C)∙hm⁻², 0.56 t(N)∙hm⁻², and 24.68 t(P)∙hm⁻², respectively. The SOC, TN, and AP storage in NPK increased by 0.64 t(C)∙hm⁻², 0.16 t(N)∙hm⁻², and 29.00 t(P)∙hm⁻², respectively. This shows that the fertilizing effect of pig manure was significantly higher than that of direct straw return; and the effect of direct straw return on the expansion of carbon and nitrogen pools was significant, but direct straw return had a minor effect on the construction of an effective phosphorus pool. Under the fertilization level of this study, the application of chemical fertilizer alone can maintain the basic balance of soil organic carbon and nitrogen pool, and have a significant effect on phosphorus pool expansion. Compared to NPK, MNPK and SNPK significantly increased the contents of soil labile organic carbon (LOC) and resistant organic carbon (ROC), and significantly increased the proportion of active organic carbon in total organic carbon; thus, the ratio of LOC+DOC to TOC increased from 9.2% of NPK to 19.0% (MNPK) and 16.3% (SNPK), respectively. The results showed that the recycling of nutrients based on the application of chemical fertilizer not only promoted the accumulation of a stable carbon pool but also expanded the soil active carbon pool, which played a positive role in improving the fertilizer conservation and supply capacity of soil. Based on the effects of different fertilization methods on the composition of the soil nitrogen pool, the contents of soil nitrate, ammonium, and total nitrogen supply capacity in the MNPK treatment was higher than those in the SNPK treatment, whereas the SNPK treatment had a significantly higher amino-sugar-nitrogen content than MNPK. This indicates that straw return was more favorable for microorganisms to fix available nitrogen into the transition pool than belly return. Not only does it reduce the export risk of active nitrogen to the environment but also improves the storage and supply capacity of soil to nitrogen. In view of the complementary effect of nutrients returning to the field and straw returning directly to the field, it is suggested that organic manure should be promoted to replace part of the chemical fertilizer based on straw returning in agricultural production.