In order to increase the service life of the mobile shot blasting machine for metal surface rust removal and reduce the content of impurities in the steel shots, a recovery and separation system of mobile shot blasting machine was optimized and improved. The coupling method of computational fluid dynamics (CFD) and discrete element method (DEM) was used to simulate and analyze the recovery and separation process. The recovery and separation efficiency were introduced as quantitative measurement parameters. The influences of airflow velocity, baffle structure, and shot blasting amount on the recovery and separation efficiency were studied, and simulation verification was conducted respectively. Results show that airflow velocity and baffle structure have a significant impact on enhancing the recovery and separation efficiency. Steel shot recovery efficiency of the optimized recovery and separation system is more than 95%, and separation efficiency of impurities is more than 80%. The maximum error between experimental results and simulation results is less than 3%, verifying the rationality of numerical simulation and providing theoretical support for optimization of structure and process parameters of mobile shot blasting machine’s recovery and separation system.