Abstract: Due to stable operation and high pumping speed, cryopumps are widely used in semiconductor manufacturing, scientific apparatus and space environment simulators. The cold plate array of a cryopump, as the main component for pumping hydrogen, significantly influences its pumping performance. This study focuses on a G-M cryocooler-based cryopump, based on rarefied gas dynamics to comparatively analyze the impact of different numbers of cold plate layers and diameters on pumping performance by angular coefficient method. The ideal cold plate array structure is selected based on three indexes: pumping speed, cooling down time and operational lifespan. Subsequently, a thermal-fluid coupling analysis is conducted on the cryopump using the ideal cold plate array, comparing the effects of different installation heights of the second-stage cold head in the G-M cryocooler on temperature distribution, pumping capacity and average pumping speed. The results indicate that for a small-diameter cryogenic pump with a nominal bore of 250 mm, a cold plate array consisting of 9 layers with a diameter of 180 mm should be installed. The advantages and disadvantages of different cold head installation positions are also discussed. The methodology presented in this study provides a theoretical basis for analyzing the pumping performance of cryocooler-based cryopumps, and the findings offer theoretical support for the development of new cold plate array structures in such pumps.