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Based on ecological crop nutrient deficiency and compensation effect theory, the nitrogen (N)-sensitive stage of rice was selected to study N deficiency at the tillering stage and N compensation at the young panicle differentiation stage. Quantitative proteomics was used to analyze leaf differentially expressed proteins (DEPs), and to investigate the leaf photosynthetic characteristics and yield under N deficiency and N compensation. The results showed that the yield per plant presented an equivalent compensatory effect (CI=1.07). The net photosynthetic rate (Pn), optimal/maximal quantum yield of PSII (Fv/Fm), soil and plant analyzer development (SPAD) value, and glutamic pyruvic transaminase (GPT) activity of T1 (N deficiency at the tillering stage, and N compensation at the young panicle differentiation stage) were lower than those of CK (N at different stages of growth by constant distribution) under N deficiency. However, after N compensation, the Pn, Fv/Fm, SPAD value, and GPT activity increased somewhat. Bioinformatics analysis indicated that DEPs that were enriched in photosynthesis, photosynthesis-antenna proteins, carbon metabolism, and carbon fixation in the photosynthetic organisms pathways were important for the maintenance of cellular homeostasis and metabolic balance in rice when subjected to N deficiency and N compensation. Moreover, the photosynthesis-responsive protein chlorophyll a-b binding protein, ribulose bisphosphate carboxylase small chain, and phosphoglycerate kinase were significantly downregulated under N deficiency. After N compensation, chlorophyll a-b binding protein, NADH dehydrogenase subunit 5, NADH dehydrogenase subunit 7, and peroxidase proteins were significantly upregulated in rice leaves. This study provides a new ecological perspective for N utilization in rice.