When simulating the flow field characteristics of the gas bearing-rotor system using the computational fluid dynamics (CFD) method, the gas film thickness is one of the crucial structural parameters. However, shape and dimensional errors arising during component machining, as well as the deviations caused by the system assembly, can lead to certain discrepancies between the actual gas film and the ideal designed gas film in terms of the spatial morphology and scale. This further affects the reliability and accuracy of the numerical calculation results. Therefore, this paper first proposed the concept of effective gas film thickness for the flow field. Through the comparative analysis and correction of the bidirectional fluid-structure interaction numerical simulation and experimental results, the reasonable equivalent gas film thickness was finally determined. The research results show that the adoption of the bidirectional fluid-structure interaction numerical simulation method can reveal the transient characteristics of the gas film flow field and the variation law of the rotor attitude, and predict and evaluate whether the gas bearing-rotor system can operate safely, saving the cost of experimental testing. The rotor inclination angle was adopted as the comparative analysis feature, providing an intuitive reference basis for the system performance deviation analysis between numerical simulations and experimental tests. The established equivalent gas film thickness maximally simplifies the numerical simulation model while enhancing computational efficiency, and simultaneously maintains reasonable result reliability. Taking a supply pressure of 0.6 MPa and a unilateral steady-state force of 80 N as an example, through error analysis and approximation, the estimated equivalent gas film thickness in the fluid-structure interaction simulation model was cyclically established and corrected. Eventually, the relative error of the system inclination angle was controlled within 5%, which greatly improved the consistency between the numerical simulation results and the performance of the actual engineering system. Furthermore, this approach provides a reliable method and basis for the application of the gas bearing-rotor simulation system in structural design, performance prediction and evaluation.