A modeling method for transverse vibration of three-dimensional (3D) orthogonally coupled plates is proposed and the through cracks located at coupling edges are considered. Corresponding experimental tests are performed to validate the effectiveness of this method. The main conflict for modeling 3D orthogonally coupled plates lies in the conflict of local coordinates of neighboring plates at the orthogonally coupled edge. The resolution of this conflict is effectively achieved by employing local collocation points method, this method is used to derive a universal expression for the coupling of plates under any coordinate system. Several cases were analyzed to compare natural frequencies, modal shapes, and dynamic responses against reference and experimental findings. Consequently, the present results are found to closely align with the measured outcomes, confirming the convergence and correctness of the proposed model and its solutions. The effects of crack parameters, such as length and number, on the vibration characteristics of orthogonally coupled plate structures are investigated. It is found that the vibrational characteristics of the coupled plates are more sensitive to the presence and variation of cracks at high frequencies. In the case of this study, as the number of cracks increases, response peaks appear at lower frequencies, with the maximum peak differing by up to twice. These findings are shown to have significant practical implications for understanding and predicting the effects of cracks in real orthogonally coupled plate structures. The effectiveness and convenience of the modeling approach for three-dimensional orthogonally coupled plates with through cracks are demonstrated in this study.