The efficiency and working performance of the motor and controller system in micro-electric vehicles depends mainly on its thermal performance, which is contingent upon effective and active cooling. The working temperature of the motor and controller may be too high during operation, which properly causes motor power reduction or motor breakdowns. Therefore, it is crucial to design a good cooling channel for better cooling the integrated motor and controller system. This work proposes an integrated cooling channel of motor and controller, and the fluid-solid coupling analysis is applied for analyzing the velocity, pressure distributions of the cooling channel, and temperature distributions of motor solid components. Meanwhile, the collaborative optimization method based on the multi-island genetic algorithm (MIGA) is used to attain optimal design parameters of the integrated cooling channel of the motor and controller for obtaining a better cooling channel design with lower flow resistance and lower winding temperatures. Results show that the original cooling channel’s flow resistance and maximum winding temperature are 31.87 kPa and 120.04°C, respectively. The flow resistance and winding temperature are pretty significant. After optimization, the local vortex flow and zero velocity area in optimal cooling channel design are improved, the coolant flow velocity becomes more uniform, and the flow resistance is significantly reduced. The flow resistance and maximum winding temperature of the optimal cooling channel design are 12.5 kPa and 116.76°C, respectively, which are decreased compared with the original cooling channel structure, with a decrease of 39.4% and 2.7%, respectively. The research findings in this work can provide theoretical reference for solid components temperature evaluation of motor and give valuable data to cooling performance evaluation and optimization of integrated cooling channel for motor and controller system.