In order to study the dynamic compression process of compressed gas in hydraulic piston compressor, the relationship between compressor structural parameters and compressor compression performance was explored. The secondary cylinder of a hydraulic piston compressor in a company's product, the pry-mounted wellhead natural gas recovery and treatment system, was taken as the research object. Based on the working principle of the secondary cylinder of the hydraulic piston compressor, the simulation process was divided into three stages, and the simulation was analyzed by Fluent software combined with the dynamic grid and UDF(user defined functions) compilation. The dynamic compression process of natural gas in the two-stage cylinder was defined, and the piston movement was taken as the evaluation index of the compressor compression performance, and the influence of the structural parameters of the two-stage cylinder on the compressor compression performance was obtained. The results show that the working stroke and lower cylinder outlet distribution have little relationship with the compression performance, and the increase of lower cylinder outlet size has a great improvement on the compression performance, and the maximum increase is 47.6%. The relevant research provides some reference for the optimization and design of hydraulic piston compressor.