Enhancing photosynthesis is considered one of the most rational strategies to increase crop yield. However, the dominant physiological driving processes of photosynthesis at different maize growth stages under long-term fertilization remain unclear. Based on a 45-years field experiment, four treatments were selected—namely, CK (no fertilizers), N (276 kg N ha−1), M (60,000 kg manure ha−1), and MN (60,000 kg manure + 276 kg N ha−1)—to study the response of maize physiological characteristics to fertilization. The results showed that long-term fertilization significantly changed the photosynthetic characteristics and endogenous hormones content. Among them, MN increased the photosynthetic rate (Pn) by 41.9–152.3% at different maize growth stages compared to CK. Organic fertilizer addition (M and MN) significantly increased superoxide dismutase (SOD), peroxidase (POD), and soluble sugar (SS) by 26.7–64.3%, 42.5–155.4%, and 16.4–89.5%, respectively. However, proline (Pro) and malondialdehyde (MDA) content decreased by 19.1–44.3% and 0.6-21.3%, respectively. Under these treatments, indole-3-acetic acid (IAA), gibberellins (GA), salicylic acid (SA), zeatin riboside (ZR), abscisic acid (ABA), SS, SOD, and POD were the main physiological driving indicators of photosynthesis. The result of PLS-SEM indicated that the main physiological driving pathways of photosynthesis were “IAA or ZR or SA-SOD-POD-Pn” and “GA or ABA-SOD or POD-SS-Pn”. Additionally, the maize grain yield of N, M, and MN increased by 111.2%, 218.1%, and 297.2% compared to CK, respectively. Overall, organic combined with nitrogen fertilizer could maintain a higher level of photosynthetic capacity by balancing endogenous hormones and enhancing the activity of antioxidant enzymes to support maize production.
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