Proton therapy in cancer treatment is an important application in nuclear science. As a key component of proton therapy, the patient positioning system (PPS) based on a robotic arm is used in cancer treatment. The PPS delivers the patient to the target position remotely for treatment with high accuracy. As a high safety and stability device in proton therapy, seismic load is one of the relevant accidental events that will affect the structural integrity of the PPS. In this study, a finite element model was built to investigate resistance of the PPS structure against seismic load. Two kinds of analysis methods (equivalent static analysis and response spectrum analysis) were carried out to calculate the displacement and stress fields to check the response of the PPS against the defined seismic load. The results indicated that all the stresses are lower than the permissible limits and the safety requirement.