Litter decomposition is a vital link between material circulation and energy flow in forest ecosystems and is intensely affected by global change factors, such as increased nitrogen (N) deposition and altered precipitation regimes. As essential nutrients, calcium (Ca), magnesium (Mg), and manganese (Mn) play crucial roles in plant energy metabolism, photosynthesis, and membrane transport of plants, and the major source of these nutrients is litter decomposition. However, the dynamics of Ca, Mg, and Mn during decomposition have been largely ignored. Thus, to better understand Ca, Mg, and Mn dynamics during leaf litter decomposition in the scenario of increasing N deposition and decreasing precipitation, we carried out a two-year field litterbag experiment in a natural evergreen broad-leaved forest in the central area of the rainy area of Western China. Two levels of N deposition (ambient N deposition and 150 kg·N·ha−1·y−1) and precipitation reduction (no throughfall reduction and 10% throughfall reduction) were set, i.e., control (Ctr: without nitrogen deposition or throughfall reduction), N deposition (N, 150 kg·N·ha−1·y−1), throughfall reduction (T, 10% throughfall reduction), and N deposition and throughfall reduction (NT, 150 kg·N·ha−1·y−1 and 10% throughfall reduction). We found that leaf litter Ca concentration increased in the early decomposition stage and then decreased, while Mg and Mn concentrations generally decreased during the whole period of decomposition. The amount of Ca showed an accumulation pattern, while Mg and Mn generally showed a release pattern. N deposition and throughfall reduction affected the Ca, Mg, and Mn dynamics, varying with different decomposition stages; i.e., N deposition significantly affected the concentration and amount of Ca, regardless of the decomposition stages, while throughfall reduction significantly affected the Ca concentration in the whole and early decomposition stages. N deposition significantly affected the concentration and amount of Mg in the whole and early decomposition stages, while throughfall reduction had no significant effects. Throughfall reduction significantly affected the concentration and amount of Mn in the whole and late decomposition stages, while N deposition had no significant effects. Ca concentration generally showed a significant positive linear relationship with mass loss in the early decomposition stage; Mg concentration showed a significant positive linear relationship with mass loss in the Ctr and N treatments in the early and late decomposition stages; Mn generally showed a significant negative linear relationship with mass loss, regardless of the decomposition stage. Overall, the results suggest that Ca accumulation is more likely affected by N deposition, while Mg and Mn releases are more likely affected by N deposition combined with throughfall reduction, particularly in the early decomposition stage.