We develop a novel three-dimensional (3D) numerical model for rigorously simulating mutual coupling effects on the channel capacity of the multiple input multiple output (MIMO) systems. In this model, the efficient integral equation method mutlilevel Green's function interpolation method (MLGFIM) is for the first time employed to calculate the input admittances and radiation patterns of the transmit and receive antennas of MIMOs. Comparing with the method of moments whose complexity is O(N2) , MLGFIM has an efficiency of O(NlogN) and is suitable for efficiently solving antenna arrays problems. To accurately model the EM wave propagation, we (1) use the ray tracing method to obtain the multi-paths and (2) rigorously obtain the dyadic path loss factor model from which a novel stochastic path loss model that is flexible for both the environments with PEC walls and that with infinite thick lossless dielectric walls is devised. Using the proposed model, we successfully analyze mutual coupling effects on the 3D correlation of a 2-by-2 monopole array and the indoor channel capacity of a 20-by-20 planar array and a 20-by-20 icosahedron array. The numerical examples in this paper demonstrate the efficiency of our model for simulating the MIMO system with complex radiators.