This paper demonstrates an advanced cross-section model including a control rod depletion for the soluble boron-free operation of small modular reactors (SMRs), specifically utilizing the STREAM/RAST-K two-step code system. With the growing demand for SMRs and the shift toward boron-free operations, control rods are essential for controlling excess reactivity. However, the insertion of control rods changes the neutron spectrum and depletes both the fuel and control rod material, necessitating a more accurate modeling approach. It is impossible to adequately address the effects of control rod insertion during fuel depletion using traditional cross-section model from two-step code system. In advanced cross-section model, the microscopic cross-section and number density changes caused by fuel and control rod depletion is possible to track. Also, this approach combines crosssection set from both rodded and unrodded fuel depletion using a history index variable. The new method is verified against whole core transport code (STREAM3D) using multi-cycle depletion calculations of SMRs, showing improved accuracy in control rod worth and power distribution predictions. Although reactivity predictions showed similar accuracy due to error cancellation, the overall method enhances precision in reactor physics calculations.