In this paper two theorems with theoretical and practical significance are given in respect to the preconditioned conjugate gradient method(PCCG). The theorems discuss respectively the qualitative property of the iterative solution and the construction principle of the iterative matrix. The authors put forward a new incompletely LU factorizing technique for non-M-matrix and the method of constructing the iterative matrix. This improved PCCG is used to calculate the ill-conditioned problems and large-scale three-dimensional finite element problems, and simultaneously contrasted with other methods. The abnormal phenomenon is analyzed when PCCG is used to solve the system of ill-conditioned equations, It is shown that the method proposed in this paper is quite effective in solving the system of large-scale finite element equations and the system of ill-conditioned equations.