Abstract: To address the high operating costs in rural freight bus logistics, and thereby improve subsidy efficiency and promote rural economic development, this study investigates the optimal government subsidy strategies and their key influencing factors. A Stackelberg game model is constructed with the government as the leader and logistics service providers as the followers. Three scenarios are compared: no subsidy, infrastructure subsidy, and operational mechanism subsidy. The influence of consumer price sensitivity, regional economic spillover effects, and subsidy intensity on the decisions of each party is then analyzed. Results show that the infrastructure subsidy widens the profit gap between the two types of logistics service providers, while freight bus operators consistently achieve higher profits under the operational mechanism subsidy. The operational subsidy is more efficient when the subsidy intensity is low, whereas excessive intensity can lead to government fiscal deficits. Conventional logistics providers benefit from the infrastructure subsidy in regions with low price sensitivity and limited funding, but can indirectly benefit from the operational subsidy in regions with high price sensitivity and greater subsidy allocations. Based on these findings, region-specific targeted subsidies are recommended, with priority given to operational subsidies in underdeveloped areas. This study fills the theoretical gap between logistics subsidies and rural revitalization, providing references for the sustainable development of rural logistics.