The safety of civil aircraft design is mainly guaranteed by the combination of finite element (FEM) analysis and experiment, the FEM analysis is an supplement to the experiment, while the experiment is a demonstration to the FEM analysis. Based on the principle of equivalent stiffness, the FEM modeling of beam structures in civil aircraft design are usually simplified to the combination of rod elements and shear plane elements, which ensures the stiffness of the FEM cross-section almost equal to the designed section, however the area of the two sections are not equivalent, thus the FEM results can not accurately reflect the stress in critical positions. To address the deficiencies in the existing method, a new method in which the height of the FEM cross-section is modified to realize stiffness equivalence is proposed in this article, the computation results of the traditional method and the proposed method are compared to analytical results, which demonstrates the accuracy of the proposed method.