A novel series input multiple outputs modular auxiliary power supply and its control strategy are proposed and investigated in this study. It adopts series input multiple outputs connection mode, where multiple auxiliary power modules are connected in series at the input side while they are independent at the output side. This auxiliary power supply can provide power for the control and drive circuits of the power modules in the input series modular system. To ensure input voltage sharing (IVS) between each module, a novel control strategy called master–slave peak current mode control strategy is proposed. With this control strategy, not only IVS can be achieved without any external central controller, but also the output controller and the IVS controller can be decoupled from each other when the system is running in discontinuous conduction mode. The stability of the control strategy is analysed, the effectiveness of the system is discussed and the design process of the controller is given. A two-module auxiliary power supply system prototype is fabricated and tested. The experimental results verify the effectiveness of the proposed system scheme and control strategy.