Abstract Changes in field management and climate will alter soil organic carbon (SOC) and nitrogen (SN) cycling in the coming decades. This study is to quantify the effects of various fertilisation strategies and climate change scenarios on crop yield, and soil C and N cycling by the end of this century. Data from a long-term experiment with a winter-wheat (Triticum aestivium L.) and summer maize (Zea mays L.) rotation in Northern China was used to calibrate and validate the SPACSYS model. Five fertiliser practices were used: control (CK); combined mineral nitrogen, phosphorus and potassium (NPK); NPK plus manure (NPKM); high application rate of NPK fertilisers plus manure (hNPKM) and NPK with straw incorporation (NPKS). Crop yields, and SOC and SN stocks by 2100 were predicted under four climate scenarios (Baseline, RCP2.6, RCP4.5 and RCP4.5). Results showed that the SPACSYS model can adequately simulate the dynamics of SOC and SN stocks and the yields of winter wheat and summer maize. An application of NPK plus manure or straw not only enhanced crop yield, but also substantially increased SOC and SN stocks. The predictions showed the positive effects of fertilisation and climate change on crop yields and SOC stocks compared with those under the baseline. However, SN stock under the RCP8.5 decreased by 3–14% by 2100 for various fertilisation strategies compared with that under the baseline. On the other hand, mineral fertiliser plus manure led to a higher soil respiration rate and nitrogen losses through leaching and surface runoff under all the climate scenarios. Therefore, application of mineral fertilisers plus manure could enhance crop productivity and sustain soil fertility but cause more carbon emitted to the atmosphere and nitrogen losses. More attention should be paid on optimising fertilisation in order to increase crop productivity while minimising environmental risks.