This study focuses on the interaction mechanism between regional economic growth and eco-agricultural benefits under water resource constraints, and takes County Yunyang as a typical case for empirical analysis. Based on the SEM method of structural equation modeling, the complex relationship between latent variables is quantified by integrating multi-source data, and the path of water resource constraints on the synergistic development of the system is revealed. The results show that the direct effect of agricultural resource endowment on the coupled state is significant, with a path coefficient = 0.731, P = 0.011, and indirectly drives the standardized impact coefficient of economic benefits η through the coupled state of 3.722. The negative effect of industrial posture on economic benefits, with a path coefficient = -4.683, P = 0.020, suggests that an over-reliance on the traditional agricultural model may inhibit the ecological benefits. The model fitness test showed that the chi-square degrees of freedom ratio x²/df=1.384, goodness-of-fit index GFI=0.947, and root mean square of approximation error RMSEA=0.057 met the statistical standard, verifying the reliability of the theoretical framework. The degree of coupling and coordination of ecological-agricultural-economic systems in Yunyang County continued to increase from 0.578 in 2015 to 0.694 in 2024, with an annual average growth rate of 1.2%, reflecting the synergistic effect of policy optimization and resource integration. This study provides a quantitative basis for the synergistic development of regional economy and eco-agriculture under water resource constraints, and realizes the coupled optimization of eco-agriculture with resources and economy.