In response to the unclear two-way interaction mechanism between technological innovation and food security in agricultural enterprises, as well as the lack of empirical testing on the mediating and synergistic effects of supply chain management and risk control, this paper uses balanced panel data and agricultural enterprise data from 31 provinces in China from 2010 to 2023 as samples, and conducts empirical analysis using panel regression and structural equation modeling (SEM). The two-stage least squares method (2SLS), propensity score matching (PSM), and bias corrected bootstrap method are combined to handle endogeneity and test robustness. The research results indicate that the overall standardization effect of technological innovation on food security should reach 0.61, with a direct effect of 0.28. The indirect effects through supply chain management and risk control are 0.21 and 0.12, respectively, with indirect spillover effects accounting for over 54%; There is a significant bidirectional promotion relationship between the two, with a reverse path coefficient of 0.22 for the impact of food security on technological innovation; The interaction coefficient between supply chain management and risk control is 0.022, indicating a significant synergistic enhancement effect. The study reveals the complete mechanism of “technological innovation management optimization risk mitigation food security”, which can provide theoretical support and decision-making reference for the national food security strategy.