Under the context of global climate change, it is critical to understand future soil organic carbon (SOC) dynamics and the corresponding diffuse phosphorus pollution, and to explore their driving factors to facilitate sustainable soil and water management in agricultural watersheds. With the integrated application of the Denitrification-Decomposition (DNDC) and Soil and Water Assessment Tool (SWAT) models, we simulated the long-term changes in SOC and diffuse phosphorus loss during the 2011–2100 period in Naoli River watershed, which is a typical agricultural watershed in northeastern China. The results showed that approximately 14.71 % of the study area will be converted from natural land (i.e., forest, pasture, and wetland) into agricultural land, and 23.50 % of the uplands will be converted into paddy fields under future climate change conditions. Without additional carbon input, the SOC will decrease at an annual rate of 0.37 % from 24.48 g/kg in 2011 to 17.77 g/kg in 2100, indicating serious land degradation in the future. As a result, watershed diffuse phosphorus loss will increase in the first 40 years (from 2011 to 2050), but show a decreasing trend in the later 50 years (from 2051 to 2100). Overall, watershed diffuse phosphorus loss will decrease from 2.75 kg/ha to 2.24 kg/ha during the 2011–2100 period. According to the scenario comparison, the logarithmic mean Divisia index and structural equation model analysis indicated that climate-induced land-use changes was the dominant factor causing SOC changes and diffuse phosphorus pollution, rather than climate change alone. The expansion of paddy fields could mitigate diffuse phosphorus pollution in the future, and improving agronomic management, such as increasing carbon inputs and integrating water and fertilizer management, are suggested to be adopted to mitigate land degradation by increasing SOC sequestration.