The stiffness of composite laminates is easily affected by wrinkle defects. In this paper, a new effective analytical model was proposed to predict the three-dimensional equivalent elastic properties of multidirectional composite laminates with wrinkle defects. Firstly, a geometric model was established according to the microscopic characteristics of wrinkle defects. Then, based on the classical laminate theory and homogenization method, the constitutive equation and flexibility matrix of the wrinkle region were established. Finally, the equivalent stiffness parameters of unidirectional and multidirectional laminates were derived, and the effects of different wrinkle parameters and ply-stacking sequences on the stiffness of unidirectional and multidirectional laminates were studied by using the analytical model. The results show that the mechanical properties of the lamina and laminates are affected by the out-of-plane angle and in-plane angle of the wrinkle defects. The accuracy of the analytical model has been verified by the numerical model and other theoretical models, and it has the characteristics of few parameters and a high efficiency. The analytical model can be used to predict the stiffness of composite structures with wrinkle defects simply, effectively, and quantitatively. It can also be used as a tool to provide the mechanical response information of laminates with wrinkle defects.