The allocation mechanism of transit subsidy in this study is to subsidize the transit operators by route. Routes can be class fled into service routes and non-service routes, and deficit-base subsidy and performance-base subsidy will be used for these routes respectively. This study considers both the formula subsidy and discretion subsidy. The subsidy allocation problem is formulated as the bi-level government decision making model. The objective of each local government is to maximize its local benefit of subsidy while the central government is to minimize the difference of the subsidy effects among local governments and subject to subsidy budget constraints. The results of case study show that the change of parameters: the ratio of formula subsidies for the operators and the ratio of matching funds to total subsidies, will affect the results of selecting the projects and allocating the subsidies. Besides, the weight of project-benefit for service routes over non-service routes will affect the probability of selection between two kinds of projects.