This article is based on the spindle reliability test bench, which carries out a thorough study on the rotor system misalignment. Misalignment is one of the most common malfunctions in the rotor system, which seriously affects its reliability. When misalignment occurs, the diaphragm group will deform to compensate for the misalignment between the driving shaft and the driven shaft, but the deformation will generate additional load. When the degree of misalignment is more serious, the additional load will affect the stability of the test bench. Due to lack of research on diaphragm couplings, there is no concrete formula of additional load caused by misalignment. In this article, the mechanism of additional load is expounded, which is based on the force and deformation analysis method. And the formulas of deformation in different misalignment conditions are deduced. Through the combination of Workbench simulation and experimental verification, the axial stiffness and radial stiffness of the diaphragm coupling are solved, and the formulas of the additional load are derived. The misalignment characteristic signals are analyzed theoretically, and the monitoring system of misalignment characteristic signals is established. Through experiments, we study the characteristics and influence of the misalignment error value in various misalignment conditions.