Little is known about the importance of long-term fertilization in crop production and nutrient leaching under heavy wet nitrogen (N) deposition from the atmosphere (WNDA) in tropical and subtropical soils. Thus, a 15-year (2004–2018) field experiment was established on a yellow soil (Orthic Arisols) near Zunyi, Southwest China, to compare the effects of fertilization on maize yields and nutrient leaching in a rotation system of summer maize-winter wheat-summer flue-cured tobacco (or sometimes sweet potato). All crops in this system received no fertilizers (CK), only chemical fertilizers (CF), or manure plus chemical fertilizers (MCF). MCF achieved higher yield and economic efficiency of fertilizers than CF after the first four maize cropping seasons. These results suggested a positive interaction between manure and chemical fertilizers. Maize plants used residual nutrients in the soil from the previous fertilizer management, which may interfere with manure efficiency. MCF alleviated soil acidification and increased soil organic matter (OM), available nutrients, microbial biomass, and enzyme activities (urease and phosphatase compared with CK and invertase and catalase compared with CF). The stimulation of microbial growth and activities may lead to OM depletion in the CF soil, while OM added into the soil in the MCF treatment may exceed microbial OM consumption. During the maize growing season, MCF decreased N and K leaching losses compared with CF. WNDA accounted for 10–12% of N fertilized to maize and 32–69% of maize N uptake in the unfertilized soil. WNDA may thus be an important N source of maize in N-poor soils.