The deviation of the effective resonance cross section obtained by conventional equivalence theory for a heterogeneous system is analyzed. It is shown that several approximations commonly adopted in conventional equivalence theory account for the deviation at different levels, with the narrow resonance (NR) approximation being the main source of deviation. Based on the analysis, an improved method based on equivalence theory is proposed. It utilizes the resonance fine flux integral table to minimize the deviation caused by NR approximation. The validity of the method is confirmed by test calculations of effective resonance cross sections in different geometries and different energy group structures. The results of eigenvalue calculations on typical fuel pin cells show that the proposed improvement is effective in reducing the error of infinite multiplication factors of the pin cell. Since the resonance fine flux integral used in this method has already been obtained in calculating the resonance integral table and can be pre-tabulated in the process of generating the library, the implementation of the proposed method is simple and requires no additional calculations. It is useful for improving the accuracy of lattice physics codes based on the equivalence theory.