The invention discloses a traction power source system of a rail transit system and a control method thereof. The method comprises the following steps that after a starting signal of a train is received, the charged state of an energy storage unit is obtained and is judged; if the charged state of the energy storage unit is in a preset range, the train is allowed to start for operation, and when the train is in a normal traction state or a normal braking state, the output current of the energy storage unit is controlled to be 0; a two-way rectifier is controlled to operate in a constant direct-current current mode; the traction powder is provided for the train through the two-way rectifier; or the braking power of the train is recovered through the two-way rectifier, wherein a constant current target value of the two-way rectifier is equal to a work current value of the train. The method has the advantages that the output current of the energy storage unit is controlled to be 0, so that the voltage of a direct current contact net can be enabled to be constant; in addition, the two-way rectifier operates in the constant direct-current current mode; the dynamic response speed is high; the output voltage fluctuation range is small.