There have been few studies on the impact of nitrogen deposition on paddy field ecosystem; therefore, we evaluated the effects of different N deposition levels (0, 40, and 120 kg N·ha−1) with the conventional nitrogen rate (180 kg N·ha−1) on rice field ecosystem through two-season experiments. The results showed that 40 and 120 kg·ha−1 nitrogen deposition had no significant effect on rice yield, although the rice grains per panicle and the 1000-grain weight increased. The 40 and 120 kg·ha−1 nitrogen deposition levels had no significant effect on rice and soil total carbon/total nitrogen (TC/TN) in the two-season experiment; however, 40 and 120 kg·ha−1 nitrogen deposition significantly increased TP content of the rice root and soil in a short time, and continuous 120 kg·ha−1 nitrogen deposition significantly decreased TP content of the rice root and significantly increased TP content of the rice stem. In addition, nitrogen deposition significantly reduced total carbon/total phosphorus (TC/TP) and total nitrogen/total phosphorus (TN/TP) in the soil. The activities of soil acid phosphatase (S-ACP), β-glucosidase (S-β-GC), and N-acetyl-β-D-glucosidase (S-NAG) increased under 40 kg·ha−1 nitrogen deposition, while the activities of S-β-GC and S-NAG decreased under 120 kg·ha−1 nitrogen deposition compared with 40 kg·ha−1. The microbial carbon, microbial nitrogen, microbial phosphorus, and fungal microbial biomass reduced under 40 and 120 kg·ha−1 nitrogen deposition. These findings suggest that, under short-term N deposition, rice and soil can adjust the C, N, P, and even the nutrient balance by themselves; however, continuous nitrogen deposition may have adverse reactions to microorganisms, thereby disrupting this balance and ultimately leading to the deterioration of paddy soil environment and a reduction in rice yield in the long term.