Two methods named Direct method and Complete method were established based on the commercial finite element software, to resolve the critical speeds calculation problem of counter-rotating rotor system and satisfy the design requirement of rotor dynamics. The basic theory and calculation process of two methods were presented in detail with a typical two spools system, while the results were verified by Harmonic response analysis. Results exhibit that the Complete method based on the eigenvalues analysis of finite element software could distinguish curves of forward or backward procession easily without any information of vibration modes, which means the solving process could be simplified significantly. The Direct method was carried out on the matrices drawn from finite element software, and all the critical speeds could be acquired by only single eigenvalues calculation without iterations. The critical speeds of a typical two spools system obtained by Direct method, Complete method and Harmonic response are exactly the same. When two spools are counter-rotating, forward procession curves descend with the increased absolute rotational speed value of the rotor which is not the excitation source. Therefore, the critical speeds are totally different from those obtained from co-rotating spools, and the dynamic characteristics of counter-rotating spools must be designed carefully. © 2021, Editorial Department of Journal of Propulsion Technology. All right reserved.