This article presents a dual‐winding permanent magnet generator (PMG) system with integrated dual‐channel controller to meet the requirements of high power density, high reliability, and high output performance of aircraft electric power system. The dual‐winding of the PMG are designed to have the same phase spatially, with which the same rotor position can be applied in independent vector control. In addition, a dual‐channel controller is applied to control the two sets of windings, which achieves high‐performance control under normal state and fault‐tolerant control under fault state. The integrated dual‐channel controller integrates two sets of main power circuits into one controller and uses a main control unit, which simplifies the PMG system leading to reduction in the overall volume and weight. Reliability analysis of dual‐winding PMG system is proposed to be compared with that of the single‐winding PMG system. A dual‐winding cooperative control strategy and a fault‐tolerant control strategy are proposed to achieve high‐performance control of DC‐link voltage under normal condition and redundant functions under fault condition. As a result, the reliability of the PMG system is improved. The experimental results validate the effectiveness of the proposed PMG system and the control strategy.