To effectively deal with the uncertainty of the benefits brought by the passenger flow risk in rail transit PPP projects, and reasonably determine the amount of capital compensation, based on the full life cycle perspective of rail transit PPP projects, this paper researched on the capital compensation decisions under the minimum passenger flow guarantee clause provided by government departments. First, with the combination method of real options and game theory, considering the acceptability of capital compensation of heterogeneous investment entities, a capital compensation decision model and cooperative game model for rail transit PPP projects under the minimum passenger flow guarantee were constructed and the feasible region and equilibrium solution of capital compensation were obtained; then, through a case study, it was verified that compared to the situation without minimum passenger flow guarantee, the constructed capital compensation decision model has less capital compensation amount and project investment threshold, but the project investment value is larger; and equilibrium solution of capital compensation has a positive correlation with the social benefit coefficient, a negative correlation with the government minimum passenger flow guarantee value and the concession period, and the investment threshold has a positive correlation with the passenger flow fluctuation rate. © 2020, Central South University Press. All rights reserved.