Intensively managed Camellia oleifera plantations with acidified soil rely on nitrogen (N) fertilizers for high yields, but this accelerates soil acidification and boosts emissions of nitric oxide (NO) and nitrous oxide (N₂O), endangering long-term sustainability. Green manure (GM) serves as an eco-friendly alternative, improving soil fertility and increasing ecosystem carbon and N inputs. However, the effects of GM species, legumes (Leg), gramineous (Gra), and their mixture (Leg-Gra) with residue incorporation on soil acidification and NO/N₂O fluxes remain unclear. To clarify the mechanisms underlying GM intercropping with residue incorporation on soil NO and N₂O emissions, we conducted an in situ study in intensively managed C. oleifera plantation ecosystems intercropping Leg, Gra, and Leg-Gra, or managed with N, manual weeding and natural grass to investigate how GM intercropping with residue incorporation influences soil acidification and NO/N₂O emissions. 1) GM intercropping with residue incorporation reduced both NO and N₂O emission rates compared to N. Specifically, Leg, Gra and Leg-Gra intercropping reduced the emission rates of N₂O by 24.83%, 46.06% and 35.64% compared to N, respectively. 2) GM intercropping reduced the abundance of AOA and AOB genes, increases the abundance of nosZ, and decreases NO and N₂O emissions. 3) Leg-Gra intercropping with residue incorporation increased soil organic carbon (SOC) by 9.96% and raised soil pH to 4.89, representing a 5.81% increase over N treatment. 4) Leg-Gra increased the decomposition rate of leguminous GM, accelerating nutrient release. Legume-gramineous intercropping effectively mitigates soil acidification, enhances SOC, and curbs NO/N₂O emissions, offering a sustainable strategy for acidic agroforestry soils.