The risks of climate change and soil degradation for the agricultural environment and crop production are increasingly prominent. Based on the limitations of land resources, it is important to explore a sustainable and effective fertilization strategy to reduce risks and ensure there is a high yield of grain and sustainable development of agriculture. Soil fertility underpins cultivated land, which is the most important resource of agricultural production, and is also the key for maintaining agricultural sustainability. The central elements of soil fertility are soil organic carbon (SOC) and soil nitrogen (SN). This study applied the Decision Support System for Agrotechnology Transfer-Cropping System Model (DSSAT-CSM) and the CENTURY-based soil module to simulate the trends of crop yields, SN storages and SOC storages until the end of this century under different climate change circumstances, based on a 36-year long-term experiment established at Shenyang site, China. Four fertilizer practices were applied: control (CK), combined chemical fertilizer of nitrogen, phosphorus, and potassium (NPK), NPK with manure (MNPK), and NPK fertilizers plus a high application rate of manure (hMNPK). The outcomes indicated that the DSSAT model can fully simulate the yields of maize and soybean as well as the dynamic stocks of the SN and SOC. Three Representative Concentration Pathways (RCP 2.6, RCP 4.5, RCP 8.5) for future development were chosen from the fifth assessment report of the United Nations Intergovernmental Panel on Climate Change (IPCC). Moreover, a baseline was installed. Crop yields, SN, and SOC storages from 2016 to 2100 were estimated under four climate scenarios (RCP 2.6, RCP 4.5, RCP 8.5, and Baseline). The RCP scenarios in some treatments reduced SN and SOC stocks and maize yield, and had no effect on soybean yield. However, the application of NPK with manure could improve crop yields, while it increased SN and SOC storages substantially. To some extent, the negative effects of climate scenarios could be mitigated by applying manure. In the RCP 4.5, maize yields of NPK, MNPK, and hMNPK treatments declined by 14.8%, 7.7%, and 6.2%, respectively, compared with that of NPK under Baseline. The NPK fertilizers plus manure treatments could cut the reduction of maize yield caused by climate change in half. Additionally, the SOC storage and SN of chemical fertilizers plus manure treatments under RCP scenarios increased by 20.2%–33.5% and 13.7%–21.7% compared with that of NPK under baseline, respectively. It was concluded that a rational combination of organic and inorganic fertilizer applications is a sustainable and effective agricultural measure to maintain food security and relieve environmental stresses.
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