To solve the very challenge problem of testing the residual acceleration with a single part of the inertial sensor, a low-cost actuation system based on hardware-in-the-loop simulation of the inertial sensor for space gravitational wave detection was designed in this study. The system combines the actuation circuit with the Simulink model. The displacement sensing, probe, and drag-free model were built in Simulink to form a closed loop with the actuation circuit through the serial port. The simulation and test results show that the hardware-in-the-loop simulation system can preliminarily test the residual acceleration of test mass, and the residual acceleration introduced by the actuation circuit is 6×10-14 m/s2/Hz1/2. Compared with the conventional test method, the system has the advantages of low cost, simple implementation, and easy extension to test any single module of the inertial sensor.