The deviations brought by the embedded self-shielding method with the pseudo-resonant isotope model is investigated. Numerical results show that error sources mainly come from the inconsistency in the heterogeneous resonance integral (RI) generated in the two-dimensional square pin–cell case with reflective boundary conditions. The high-order resonance interference effect also contributes to the deviation. The black assumption on the macroscopic cross section of the fuel is proposed to enhance the consistency in the generation of the heterogeneous RI table. Numerical results show that the modification on the original embedded self-shielding method improves the accuracy of the cross-section prediction in the multifuel lattice systems.