In the simulation of the accelerator magnet support system, the parts connected to the ground by the magnet bracket are usually treated as “fixed”, but in some cases, this treatment will cause a large error between the simulation results and the measurement results. This paper proposes an indirect method to measure the contact stiffness of rough surface, accurately quantify the contact stiffness of rough surface, and make the simulation of the whole system well match with the test results. Based on the contact stiffness model, ANSYS finite element simulation method and modal test method, the accuracy of indirect measurement method was verified by taking the test piece of anchor bolt fixation method as an example, so that the contact stiffness was accurately quantified. This method can also provide a basis for improving the overall stiffness of the accelerator magnet support system.