There are many numerical methods for simulate three-dimensional photonic crystals, after comparison, we choose Yee's scheme to be our discrete method. So far, this method can only be applied to simple cubic lattice and face-centered cubic lattice, but there are 14 Bravais lattices in three-dimensional space. In this paper we extended Yee's scheme to all of the 14 Bravais lattices. After discretization, we get a general eigenvalue problem, and we will analyze this general eigenvalue problem. The second important task of this paper is to find the eigen-decomposition of the discrete curl operator, after a series of complicated calculations, we find that all the lattices can be summed up into two kinds of decomposition. We are interested in finding the several few smallest real eigenvalues, but the large dimension of null space is 1 3 of all, this seriously affected the convergence of calculation, we use a technique which is called nullspace-free method to avoid this trouble. But this technique transforms the sparse matrix in our problem to a dense matrix, fortunately, the eigenvectors we found before are related to discrete Fourier transformation. The efficiency of calculation has been significantly improved by using the fast Fourier transformation. Finally, we calculate the band structures of photonic crystals on various lattices, and implement high performance calculations on the GPU.