Flexible jointed-panel structures play a significant role in the entire service cycle of spacecraft, but they also bring serious vibration problems to the spacecraft orbit control. The bidirectional flexible jointed-panel structure installed on the large-scale spacecraft considered in this paper may produce large-amplitude vibration. To investigate the nonlinear vibration of such a flexible structure, a nonlinear dynamic model with a lower degree of freedom should be established analytically. Thus, the global mode functions of such a complex structure should be extracted first. Taking the eigenfunctions of beams as basis functions, the Rayleigh–Ritz method is developed to extract the analytic global mode functions for bidirectional flexible jointed-panel structures. As a typical example, the cruciform flexible jointed-panel structures made up of six isotropic rectangular panels are investigated, and the dynamic model for the transverse vibration of the structure is established. Numerical results are conducted to illustrate the validation of the proposed modeling process by comparing the natural frequency and global modes obtained by the developed approach with those obtained from the finite element method. Then, the influence of parameters on the inherent properties of the structure is discussed, and an effective method to increase the fundamental frequency of the structure is proposed.