Forests have the largest terrestrial nutrient pools. The loss of soil carbon and nitrogen in forests under ongoing climate warming is subject to severe environmental degradation. To mitigate the negative effects of global warming on soil carbon and nitrogen in forest, it is important to obtain a better understanding of how elevated temperature and altered precipitation variability impact soil nutrient dynamics. To explore such interactions, we coupled an eco-hydrological model (Multi-Layer Canopy model, MLCan) with a biogeochemical model and applied the combined model to Pinus densiflora forest in Gwangneung Experimental Forest, South Korea, from 2004 to 2020. Our results showed that there was a time lag of 4 years to trigger soil organic carbon losses under the elevated temperature of +1.11°C during 2014–2020 compared to 2010–2013. A temperature rise over a prolonged period increased microbial biomass and activity, stimulating soil organic carbon decomposition. The combination of soil nitrate accumulation and exceptional but expected delay in heavy precipitation seasons of 2 months led to nitrate leaching four times higher than the average at 1 m depth in 2010. Reduced evapotranspiration and heavy precipitation during early fall caused intense subsurface water flux, resulting in a great increase in the risk of nitrate leaching. Our results highlight that the impacts of global warming on soil carbon decompositions has a time lag of 4 years and changes in precipitation characteristics will lead to excessive nitrate loss in P. densiflora forests under climate change.