A multiple output stage converter (MOSC) and an operating method thereof are provided. The MOSC includes a first transistor, a second transistor, a third transistor, and a logic control module. A terminal of the first transistor, a terminal of the second transistor, and a terminal of the third transistor are coupled to a power source via an inductor. Another terminal of the first transistor is coupled to a first output terminal. Another terminal of the second transistor is coupled to a second output terminal. Another terminal of the third transistor is coupled to a ground voltage. The logic control module is used to control the on/off state of the second transistor. The well of the second transistor is floating when the first transistor or the third transistor is on. The well of the second transistor is floated or coupled to the second output terminal when the second transistor is on.