The platform carrying capacity of urban rail transit stations is limited and overcrowding of the platform will lead to serious safety risks for passengers and trains. It is significant to collaborate on the optimization of passenger flow strategy and skip-stopping scheme to alleviate traffic pressure and ensure platform safety. This study proposes and solves the joint optimization problem of coordinated flow control and skip-stopping scheme considering platform carrying capacity. Firstly, platform demand constraints and platform stranded constraints are designed according to the maximum carrying capacity of the platform to control the number of allowable arrivals ensuring platform safety. Secondly, train arrival variable and train stop variable are introduced to generate train skip-stopping index. Finally, considering the characteristics of passengers' continuous arrival and platform carrying capacity, a mixed integer programming model is established to minimize the number of passengers outside the station and the number of passengers stranded on the platform. Based on empirical data, this study takes Beijing Batong line as a case study and uses the established model to generate flow control strategy and skip-stopping schemes for each station during morning rush hours. Experimental results show that compared to the baseline without implementing the two proposed strategies, the proposed collaborative optimization method can effectively reduce the demand for staying at the platform and increase the number of boarding passengers at downstream stations. Thus, the balance between train capacity and passenger flow demand is maintained while ensuring platform safety. Moreover, the proposed method can also avoid overcrowding at downstream stations.