Two or more high-voltage isolated power supplies are required for many high-voltage applications, such as in microwave generating and ion implantation. Traditionally, several separate high-voltage isolated converters are employed, which contain many components and complex control systems. This article proposes a dual-output converter, which consists of two input series connected full-bridge inverters, the two inductor-capacitor-capacitor (LCC) and two inductor-inductor-capacitor (LLC) resonant networks connected with the full-wave Cockcroft–Walton voltage multipliers and the synchronous rectifiers, respectively. Comparing with the traditional solutions, the number of switches and their peripheral circuits are reduced. By regulating the switching frequency and three phase-shift angles of the inverter, the proposed converter allows one port to operate alone or both ports to operate simultaneously, while achieving soft switching, and maintaining the voltage balancing between two input series capacitors. In this article, a detailed analysis of the operating principle and its characteristics such as the output voltage gain and soft switching are presented. Finally, a prototype with two outputs, 4–5 kV/3.8 kW and 15 V/600 W, is built to verify. The results convincingly demonstrate the applicability of offering one or two isolated outputs, which offers a high integrated, efficient, and simple solution for powering the magnetrons.