The portable rugged computer generally needs to adapt to high temperatures, hot and humid, and other harsh environments, while taking into account its portability, the machine cooling space is limited, and the motherboard carries the CPU, graphics cards, and other major heat-producing components. Therefore, some problems often occur due to the irrational design of the motherboard cooling structure, resulting in poor adaptability to high-temperature environments, arithmetic performance being difficult to fully play, and so on. In this paper, based on the use of a certain type of portable rugged computer requirements, a motherboard cooling structure is designed through the thermal structure, fan and increasing the heat dissipation area and other forms, and the type of computer cooling effect has been measured by simulation analysis and experimental verification to verify that it can enhance the cooling effect, to provide a better reference for the same type of portable rugged computer motherboard cooling structure design.