This paper presents an automatic optimization system for the heat source layout of multi-chip modules, referred to as IOS. The system aims to optimize the heat source layout of multi-chip modules through the integration of multiple software tools. The IOS utilizes an optimization algorithm, WINDOW DOS, and other methods to achieve this goal. Initially, two optimization strategies are introduced which are utilized in conjunction with the Non-dominated Sorting Genetic Algorithm-II(NSGA-II). Subsequently, a simplified thermal model of the multi-chip module is applied to the IOS. The automatic optimization module is then used to optimize the heat source layout. In the end, we simulated and analyzed the application results. The simulation analysis reveals that when the temperature extreme value index is optimized, the PCB boardās transient temperature range falls within [343.14 K, 344.09 K]. Similarly, when the temperature homogeneity index is optimized, the PCB boardās transient temperature range falls within [343.39 K, 344.21 K]. Comparing these results with the experience layout, the temperature difference is reduced by 76.36% and 79.60%, respectively. The optimization results demonstrate that the IOS has a significant impact, offering remarkable optimization effects, low cost, high efficiency, and a more uniform temperature distribution. These findings indicate that the IOS holds promising potential for applications and provides value in optimizing the heat source layout of multi-chip modules.