Abstract: The physiological response mechanism of seagrass to nitrogen and phosphorus nutrients is a key scientific issue for understanding how seagrass bed ecosystems cope with eutrophication stress. In this study, the submerged plant Thalassia hemprichii was subjected to treatments with varying nitrogen-to-phosphorus (N:P) ratios (4:1, 8:1, 16:1, 32:1). The changes in photosynthetic pigments, characteristics of material accumulation, and antioxidant enzyme activities of T. hemprichii were analyzed systematically to reveal its adaptive regulatory mechanisms in response to changes in N:P ratios. The results showed that, under the action of nitrogen and phosphorus, T. hemprichii formed a systematic physiological response network by regulating the synergy among three modules: “photosynthetic efficiency-material allocation-redox balance.” Photosynthetic pigments exhibited stage-specific functional reorganization: chlorophyll a maintained light capture efficiency through a three-stage pattern of “initial synthesis surge-mid-term photodamage degradation-late-stage chlorophyll b compensation;” carotenoids gradually decreased, with a significant decline in the third week, causing a temporary failure of photoprotective functions and triggering a cascade response of the antioxidant system. Material metabolism showed a N:P ratio-dependent carbon allocation strategy: under low N:P ratios, nitrogen was preferentially used for the synthesis of photosynthetic enzyme (Rubisco), while under high ratios, nitrogen allocation shifted toward soluble sugar accumulation. The antioxidant enzyme system achieved temporal division of labor through “immediate scavenging of superoxide anions by superoxide dismutase (SOD)-lagged degradation of hydrogen peroxide by peroxidase (POD)/catalase (CAT),” and constructed a hierarchical defense mechanism. When the N:P ratio exceeded 32:1, the decreased enzyme synergistic efficiency led to intensified oxidative damage. This study demonstrates that changes in N:P ratios drive the physiological responses of T. hemprichii essentially through the dynamic reconstruction of a multi-dimensional metabolic regulation network, providing a new paradigm for understanding the adaptation mechanisms of submerged plants to nutrient stress, and the research results provide key mechanisms supporting for the ecological restoration of seagrass beds in eutrophic marine areas.