The design principle of the cavity-based scramjet combustor is to maximize combustion efficiency while minimizing total pressure loss. An experimental cavity-based scramjet was used as Type Ⅰ-1, while Type Ⅱ-1 was derived by replacing it with a periodic combustor with evenly distributed fuel nozzles. Introducing a bypass channel resulted in Types Ⅰ-2 and Ⅱ-2, whereas arranging wedges and ramps in Type Ⅱ-1 led to Types Ⅱ-3 and Ⅱ-4, respectively. Supersonic combustions in these six configurations were studied using three-dimensional numerical simulations. The results showed that combustion efficiency at the outlet increased by 22.77% in Type Ⅰ-2 compared with Type Ⅰ-1, whereas Types Ⅱ-2, Ⅱ-3, and Ⅱ-4 increased by 18.32%, 12.31%, and -6.94%, respectively, compared with Type Ⅱ-1. Regarding total pressure loss at the outlet, Type Ⅰ-2 decreased by 1.14% compared with Type Ⅰ-1, whereas Types Ⅱ-2, Ⅱ-3, and Ⅱ-4 decreased by 2.42%, 1.46%, and 0.4%, respectively, compared with Type Ⅱ-1. The findings indicate that increasing the upstream low-speed zone, redirecting upstream airflow, and isolating airflow impact can increase the fuel jet’s Penetration Height (PH). Type Ⅰ-2 significantly increased PH through a bypass channel, whereas Type Ⅱ-3 reduced the obstruction of the fuel jets to the airflow entering the cavity through wedges, allowing oxygen-rich airflow into the cavity and maintaining combustion at the lower boundary of the fuel jets. Types Ⅰ-2 and Ⅱ-2 achieved significant bypass airflow, establishing a combustion zone near the wall downstream of the cavity and significantly reducing the temperature of the wall downstream. The results confirm that using bypass airflow to promote cavity-based scramjet combustion is a feasible approach. The shock wave structure in the scramjet combustor remains the primary contributor to total pressure loss, highlighting the importance of designing scramjet combustors with weaker shock waves.