With the increase of flight speed, the non-uniform flow distribution inside the scramjet engine leads to severe heat transfer degradation, posing greater challenges to the efficiency and flow distribution of the regenerative cooling system. A pseudo three-dimensional topology optimization algorithm considering average flow distribution is proposed to address this problem. By introducing flow deviation constraints, the generated topology effectively improves the flow uniformity in parallel channels. The results show that the optimization algorithm generates adapted topologies for different inlet flow fluctuations, and the flow deviations are all reduced by more than 93%. This resulted in a 400% increase in the inlet flow differential, while the maximum fluid temperature change rate increased by only 5.55%. The heat transfer coefficient is increased by 114.3% compared to the straight-through channel. This study provides an efficient and reliable optimization method to inhibit the inhomogeneous flow distribution and local overheating in the regenerative cooling channel.