Obtaining a holistic understanding of the impacts of atmospheric nitrogen deposition on multiple ecosystem services of forest is essential for developing comprehensive and sustainable strategies, particularly in heavy N deposition regions such as subtropical China. However, such impacts remain incompletely understood, with most previous studies focus on individual ecosystem function or service via understory N addition experiments. To address this knowledge gap, we quantified the effects of over‐canopy and understory N additions on multiple ecosystem services based on a 7‐year large‐scale field experiment in a typical subtropical forest. Our results showed continued over‐canopy N addition with 50 kg ha−1 year−1 over a period of 4–7 years significantly increased plant nutrient retention, but did not affect the services of soil nutrient accumulation, water yield, C sequestration (in plants and soil), or oxygen release. There were trade‐offs between the soil and plant on providing the services of nutrient accumulation/retention and C sequestration under over‐canopy N addition. However, without uptake and retention of tree canopy, the trade‐off between soil and plant were more weaken under the understory N addition with 50 kg ha−1 year−1, and their relationships were even synergetic under the understory N addition with 25 kg ha−1 year−1. The results suggest that understory N addition cannot accurately simulate the effects of atmospheric N deposition on multiple services, along with mutual relationships. Interestingly, the services of plant N, P retention, and C sequestration exhibited a synergetic increase under the over‐canopy N addition but a decrease under the understory N addition. Our results also found tree layer plays a primary role in providing plant nutrient retention service and is sensitive to atmospheric N deposition. Further studies are needed to investigate the generalized effects of forest canopy processes on alleviating the threaten of global change factors in different forest ecosystems.