Supercritical carbon dioxide (S-CO₂) printed circuit heat exchangers (PCHEs) are widely used in Brayton cycle power generation system, but PCHE faces problems such as uneven heat transfer and poor comprehensive performance under different working conditions. To improve the overall performance of PCHE in the Brayton cycle, the comprehensive performance (PEC) of S-CO₂ on both the cold and hot sides of PCHE under different parameters was numerically investigated, by using S-CO₂ as the working fluid, and varying the convergent-divergent pitch period (T), cross-sectional area ratio (β), and the ratio of convergent length to divergent length (γ). The results show that when β and γ are fixed, the pitch period on the cold side is inversely proportional to the overall performance, while the optimal pitch period on the hot side ranges from 15 mm to 25 mm. The PEC values of PCHE with convergent-divergent pitch periods are consistently greater than 1, indicating superior performance compared to the conventional straight-channel designs. Under a cold-side operating pressure of 22 MPa, the PCHE shows a relatively high comprehensive performance compared to the hot-side operating pressure of 8.5 MPa. When the cross-sectional area ratio β exceeds 1, all PEC values are greater than 1, and the intensified convective heat transfer between the fluid and the wall enhances the overall performance. With other conditions held constant, the system achieves better comprehensive performance when the ratio of convergent to divergent length γ is 3/7. The results provide a reference basis for optimizing the comprehensive performance of PCHE with gradually varying cross-section flow channels.