An experimental study was conducted on the direct-connect scramjet combustor experiment system to investigate the performance optimization of scramjet combustor by adjusting the shape angles and fuel injection. An orthogonal array design of experiment method was used to organize the combination of shape angles. For every combination of shape angles, five experiments with different fuel injection arrangement were carried out, and every experiment was actualized with three equivalence ratios by adjusting a throttling venturi. The test data were used to build a response surface model of the combustor performance with respect to configuration parameters for combustor configuration optimization. The optimal combustor configuration was obtained by two successive optimizations, and the effects of configuration parameters on combustor performance were analyzed. The results showed that the thrust gain of optimal combustor configuration was increased by 10.4% relative to the baseline configuration, and the combustor performance was influenced strongly by the couple of configuration parameters.