An effective three-dimensional micromagnetic method for predicting equilibrium configuration of magnetization states is presented with conjugate-gradient technique to minimize the total energy, which has a much faster convergence rate than that of the quasi-Newton method. As an application, magnetic tunnel junctions with pinholes in the ultrathin barrier are simulated. The calculated coupling field Hf increases with the pinhole density increase, corresponding to the decrease of barrier thickness. The free layer domain configuration of tunnel junction during the switching process is also demonstrated.