This study proposes a bi-level multi-objective optimization framework integrating anaerobic digestion (AD) and lipid exchange technology to address low resource efficiency, poor economics, and weak policy incentives in municipal food waste (FW) management. A government-enterprise collaborative mechanism optimizes technical processes and policy instruments. The technical strategy combines lipid exchange pretreatment with anaerobic co-digestion (AcoD), establishing a “lipid modification-methane enhancement” pathway. Experimental results demonstrate that a lipid removal ratio of 0.1 maximizes performance: lipid recovery increases to 15%, daily methane production reaches 1,155 m \(^3\) /day (23% higher than traditional AD), and economic benefits peak at 3.109 million yuan/day (35% from lipid sales, 28% from power subsidies). Optimized policy schemes (e.g., 130 yuan/ton for FW treatment and 0.25 yuan/kWh for power generation) balance fiscal costs and resource recovery. A case study validates the framework, allocating 800 tons/day to Plant A and 1,200 tons/day to Plant B, achieving an 18% reduction in Plant B’s unit cost. This work provides a sustainable solution through integrated technology-policy co-optimization.