To help solve flow mal-distribution and cooling capacity utilization problems in parallel cooling channels of SCRamjet, the variable channel sectional area design is put forward. 3D modelling of the flow and heat transfer in multiple parallel channels is carried out under supercritical pressure. The flow distribution reasonability and cooling effect under different channel sectional area designs are numerically compared and analyzed. The analysis indicates the variable channel sectional area design improves the flow distribution reasonability obviously and lowers the wall temperature. Furthermore, the variable channel sectional area design adapts to different heat flux boundary conditions. Even in the flow mal-distribution problems caused by both inlet/outlet headers and non-uniform thermal boundary, the variable cross section area design works well because the ratio of channel pressure drop which is insensitive to the heating is increased. The fuel cooling capacity utilization is also refined.