AimBiochar application is a promising strategy to mitigate water deficiency impacts on crops, yet its synergistic effects with deficit irrigation (DI) on photosynthetic fluorescence performance and seed nutritional quality and their coupling mechanism remain poorly understood.MethodsA two-year field experiment with factorial combinations of irrigation regimes [full irrigation (FI, 100% ETc) vs. deficit irrigation (DI, 60% ETc)] and biochar amendments (0, 15, 30 t ha(-)1, denoted as B0, B15, B30) were conducted in the semiarid region of China.ResultsHigh-dose biochar (B30) effectively alleviated water-stortage induced photoinhibition in Photosystem II. Compared to DI without biochar amendment, the DI + B30 treatment enhanced F0/Fm by 33.0% and Fv/F0 by 7.9%, while simultaneously reducing the inactivation of Photosystem II reaction centers as evidenced by a 6.4% decrease in Vi during 2022. Particularly noteworthy was the biochar-mediated amplification of J-phase fluorescence intensity (reflecting the accumulation of reduced primary electron acceptor QA(-)) during the O-J transition. Concurrent with these photosynthetic improvements, B30 application under DI conditions significantly elevated seed nutritional quality parameters: crude fat content increased by 5.0%, protein content by 9.6%, and proline accumulation by 6.9%. Structural equation modeling further deciphered the hierarchical relationships among key parameters, identifying Fv/F0 (total effect = 0.70), leaf area index (0.60), plant height (0.58) and aboveground biomass (0.56), as primary drivers of seed quality enhancement (R2 = 0.73).ConclusionOur findings demonstrate that the biochar-DI synergy optimizes photosynthetic resilience and nutritional value, providing a water-carbon management framework for arid farmland.Highlights center dot Biochar alleviates water deficit-induced damage to Photosystem II by enhancing chlorophyll a fluorescence parameters (Fv/Fm and Fv/F0).center dot 30 t ha-1 biochar optimizes the J-phase fluorescence intensity and boosts seed crude fat (7.5%) and arginine (8.6%).center dot Structural equation modeling deciphered the hierarchical drivers of seed quality, identifying Fv/F0 and leaf area index as the primary contributors.Highlights center dot Biochar alleviates water deficit-induced damage to Photosystem II by enhancing chlorophyll a fluorescence parameters (Fv/Fm and Fv/F0).center dot 30 t ha-1 biochar optimizes the J-phase fluorescence intensity and boosts seed crude fat (7.5%) and arginine (8.6%).center dot Structural equation modeling deciphered the hierarchical drivers of seed quality, identifying Fv/F0 and leaf area index as the primary contributors.Highlights center dot Biochar alleviates water deficit-induced damage to Photosystem II by enhancing chlorophyll a fluorescence parameters (Fv/Fm and Fv/F0).center dot 30 t ha-1 biochar optimizes the J-phase fluorescence intensity and boosts seed crude fat (7.5%) and arginine (8.6%).center dot Structural equation modeling deciphered the hierarchical drivers of seed quality, identifying Fv/F0 and leaf area index as the primary contributors.