According to the working principle and the conditions requirement of the fruit-seedling separation device of processing tomato harvester, the hydraulic system of the apparatus was designed. The main components of the hydraulic system were selected through the parameter calculation. A simulation model of the system was established through using AMESim hydraulic system simulation software, and then simulation analysis was conducted. The simulation analysis results are in good agreement with that from the test run of the system, and it can ensure the reliable operation of the fruit-seedling separation device of processing tomato harvester.