Rectangular magnetically shielded rooms (MSRs) are favored for their construction simplicity and efficient space usage. However, current rectangular MSRs lack an effective shielding factor (SF) theoretical system due to their inherent asymmetric geometry and process defects such as door gap. Therefore, an effective three-dimensional (3D) magnetic circuit method for calculating the SF of rectangular MSRs is proposed in this paper. Firstly, the theoretical model for the 3D magnetic circuit of rectangular MSRs is established, and the SF in three directions is derived. Secondly, the theoretical model is modified by introducing demagnetization factors to further improve the calculation accuracy of the SF based on the magnetization theory. Finally, formula systems for the SF considering door gap are derived, and their effect is also analyzed. To validate the proposed method, two rectangular MSRs with distinct structures are tested using a constructed experimental platform. The results show that the discrepancy between the calculated SF and the tested SF is less than 7%, affirming the efficacy of the proposed methodology. This method can be applied to rectangular MSRs of different sizes, and provide a valuable theoretical guidance for the construction of MSRs.