To develop a new microchannel cooling structure for end-pumped solid-state lasers, the temperature distribution of gain medium and flow resistance in the cooling structure were studied using the fluid-thermal-solid coupled numerical method, which provides a theoretical basis for optimization of the new cooling structure. Results show that there is no obvious decrease in maximum temperature of gain medium when the coolant flow rate increases to 15 L/min, and the flow resistance in the microchannel cooling structure at this flow rate does not dramatically influence the working condition of the cooling system. The inlet and outlet positions of the cooling structure and the flow direction greatly influence the temperature distribution of gain medium.