Linear and coaxial pulse tube cryocoolers （PTCs） are widely used in space， especially coaxial PTCs. The coaxial PTC has a compact structure and is more convenient to use， while the linear structure is simple with high cooling efficiency. At present， the research on the difference between the two PTCs based on theoretical research is relatively rare. Therefore， it is very valuable to carry out some comparative studies between the two PTCs. Two kinds of Stirling-type single-stage PTCs （in-line and coaxial type） are analyzed due to their different structures in this paper. One-dimensional numerical model is established to analyze the changes of the relevant thermodynamic parameters in the two cryocoolers. The mechanism is revealed that different structural changes could lead to different cooling performance. The differences between the PTCs are compared by analyzing the energy flows， acoustic impedance networks. Also， two experimental setups are established， and the performance of the two pulse tube cryocoolers is tested and analyzed. The results show that the in-line cryocooler has higher cooling efficiency， and the coaxial one could reach lower cooling temperature at the same input power because the pulse tube is placed in the regenerator of the coaxial system and precooled by the regenerator. By comparing the simulation data with the experimental results， it is found that there is a good consistency.