A numerical method is put forward in this paper, using the boundary element method(BEM) to model 3D terrain effects on magnetotelluric (MT) surveys. Using vector integral theory and electromagnetic field boundary conditions, the boundary problem of two electromagnetic fields in the upper half space (air) and lower half space (earth medium) was transformed into two vector integral equations just related to the topography: one magnetic equation for computing the magnetic field and the other electrical equation for computing the electrical field. The topography integral is decomposed into a series of integrals in a triangle element. For the integral in a triangle element, we suppose that the electromagnetic field in it is the stack of the electromagnetic field in the homogeneous earth and the topography response which is a constant; so the computation becomes simple, convenient and highly accurate. By decomposition and computation, each vector integral equation can be calculated by solving three linear equations that are related to the three Cartesian directions. The matrix of these linear equations is diagonally dominant and can be solved using the Symmetric Successive Over-Relaxation (SSOR) method. The apparent resistivity curve of MT on two 3D terrains calculated by BEM is shown in this paper.