To improve the heat dissipation reliability of the nuclear power control system chip, the structure of its water-cooled heat sink is compared and analyzed. Three schemes of water-cooled heat sinks are proposed, and CFD analyzes the heat dissipation performance of the heat sink. The simulation data of the heat transfer coefficient, pressure loss, and heat sink comprehensive coefficient are compared. The results show that the average temperature of the bottom surface of the three heat sinks tends to be flat with the flow velocity increase, and the heat dissipation coefficient Nu is also the same. The S-type heat sink has a higher heat transfer coefficient and lower average bottom temperature. The pressure loss of the S-type heat sink is much higher than that of the other two schemes with the increased flow rate, and the system resistance is large. By calculating the comprehensive coefficient of the heat dissipation process of the three heat sinks and considering the heat dissipation capacity and other factors, it is considered that the circular fin heat sink can be the optimal solution.