Anthropogenic nitrogen (N) emissions and deposition have been increasing over past decades. However, spatiotemporal variations of N deposition levels and major sources remain unclear in many regions, which hinders making strategies of emission mitigation and evaluating effects of elevated N deposition. By investigating moss N contents and δ15N values in southwestern (SW) China in 1954–1964, 1970–1994, and 2005–2015, we reconstructed fluxes and source contributions of atmospheric ammonium (NH4+) and nitrate (NO3‐) deposition and evaluated their historical changes. For urban and non‐urban sites, averaged moss N contents did not differ between 1954–1964 and 1970–1994 (1.2%–1.3%) but increased distinctly in 2005–2015 (1.6%–2.3%), and averaged moss δ15N values decreased from +0.4‰ to +3.3‰ in 1954–1964 to −1.9‰ to −0.7‰ in 1974–1990, and to −4.8‰ to −3.6‰ in 2005–2015. Based on quantitative estimations, N deposition levels from the 1950s to the 2000s did not change in the earlier 20 years but were elevated substantially in the later 30 years. Moreover, the elevation of NH4+ deposition (by 12.2 kg‐N/ha/year at urban sites and 4.6 kg‐N/ha/year at non‐urban sties) was higher than that of NO3‐ deposition (by 6.0 and 2.9 kg‐N/ha/year, respectively) in the later 30 years. This caused a shifted dominance from NO3‐ to NH4+ in N deposition. Based on isotope source apportionments, contributions of combustion‐related NH3 sources (vehicle exhausts, coal combustion, and biomass burning) to the elevation of NH4+ deposition were two times higher than volatilization NH3 sources (wastes and fertilizers) in the later 30 years. Meanwhile, non‐fossil fuel NOx sources (biomass burning, microbial N cycles) contributed generally more than fossil fuel NOx sources (vehicle exhausts and coal combustion) to the elevation of NO3‐ deposition. These results revealed significant contributions of combustion‐related NH3 and non‐fossil fuel NOx emissions to the historical elevation of N deposition in SW China, which is useful for emission mitigation and ecological effect evaluation of atmospheric N loading.