Intercropping with leguminous green manure represents a sustainable approach to enhance agroecosystem resilience through improved soil fertility and resource-use efficiency. However, the synergistic mechanisms between leguminous green manure intercropping and regulated deficit irrigation in maintaining maize yield stability and enhancing kernel profiles under arid conditions remain inadequately understood. A three-year (2021–2023) split-plot field experiment incorporated main plots consisting of three green manure incorporation practices: full green manure incorporation (M||V-P), green manure stubble retention (M||V-R), and maize without green manure (maize sole cropping, SM); while split plots comprised three irrigation regimes: conventional (I3; 400 mm), 15% deficit (I2; 340 mm), and 30% deficit (I1; 280 mm). The study examined maize grain yield, kernel quality (protein, fat, starch, and essential amino acid content), net photosynthetic rate (Pn) of maize, and soil nitrate-ammonium nitrogen content. M||V-P and M||V-R increased maize grain yield compared to SM, with M||V-P producing 5.7% higher yields than M||V-R. Notably, M||V-PI2 achieved comparable yield to M||V-PI3 while reducing irrigation by 15%, demonstrating an 18.3% yield increase over SMI3. M||V-P and M||V-R enhanced kernel quality compared to SM, exhibiting higher protein, fat, starch, and essential amino acid content. Decreased irrigation led to increased kernel protein content but reduced fat and starch contents. The kernel protein content under M||V-PI2 showed no significant difference from M||V-PI1, while maintaining fat, starch, and essential amino acid content similar to M||V-PI3. M||V-PI2 improved all kernel quality parameters relative to SMI3. These enhancements primarily resulted from maize intercropped with leguminous green manure in combination with 15% deficit irrigation, which increased maize Pn by 14.3%, and elevated soil nitrate-ammonium nitrogen by 12.5 and 5.2%, respectively. These findings demonstrate a scalable approach for sustainable maize production though the integration of leguminous green manure intercropping in water-limited regions.