Abstract: To address the problem of high operating costs in rural freight bus logistics, improve subsidy efficiency, and promote rural economic development, the optimal government subsidy strategies and key influencing factors are explored. A Stackelberg game model led by the government and followed by logistics service providers is constructed. Three scenarios—no government subsidy, infrastructure subsidies, and operation mechanism subsidies—are compared, and the mechanism by which variables such as consumer price sensitivity, regional economic spillover effects, and subsidy intensity affect the decision-making of all parties is analyzed. The results show that: infrastructure subsidies widen the profit gap between the two types of logistics service providers, while the profits of freight buses are always higher under operation mechanism subsidies. Operation subsidies are more efficient when the subsidy intensity is low, while excessive intensity easily leads to government debt. Traditional logistics service providers profit from infrastructure subsidies in regions with low price sensitivity and less subsidies, but can indirectly benefit from operation subsidies in regions with high price sensitivity and more subsidies. In conclusion, strategies such as targeted subsidies by region and prioritizing operation subsidies in underdeveloped regions are proposed. This fills the theoretical gap between logistics subsidies and rural revitalization and provides references for the sustainable development of rural logistics.