The numerical simulation of rough surfaces is research precondition and basis of contact capacity of engineering assemblies. Aim at the shortcoming in the simulation of rough surfaces, a new numerical simulation method of 3 D gaussian rough surface was proposed. Based on the given autocorrelation function ( ACF) , the non-linear equations were constructed for computing transformation matrix, the transformation matrix was acquired by solving the equations with the improved non-linear conjugate gradient method; The height distribution matrix of rough surface was acquired by transforming random matrix based on the transformation matrix. At last, the anisotropic and isotropic 3 D Gaussian rough surfaces were simulated by the proposed method, and the proposed method was validated by the contrast result of autocorrelation function curves.