Supersonic film cooling utilizing gaseous hydrocarbon fuel is an effective method to meet the thermal protection and drag reduction requirements inside a scramjet engine. The film injection scheme for film cooling using gaseous hydrocarbon fuel is crucial in determining the thermal protection and drag reduction performance of the film with oxidative cracking reaction. In this paper, a numerical study is conducted to compare the thermal protection and drag reduction performance of gaseous hydrocarbon fuel film under the slot injector film cooling structure and the multi-port injector array film cooling structure. The results show that the multi-port injector array film cooling utilizing gaseous hydrocarbon fuel as a coolant improves both thermal protection and drag reduction performance compared to the slot injector film cooling structure. The chemical reaction of hydrocarbon fuel expands the cooling range and low resistance area of a single discrete hole. The reason is that the multi-port injector array film cooling intermittently interrupts the oxidation and heat release process of the hydrocarbon fuel in the boundary layer, resulting in higher cooling efficiency in the film cooling injection area. It also improves the spatial distribution of the hydrocarbon fuel film, allowing for effective utilization of the chemical heat sink of the hydrocarbon fuel, which improves the thermal protection performance and expands the effective cooling area. Furthermore, the enhanced mixing of the multi-port injector array film cooling in the film injection area improves drag reduction performance through combustion inside the boundary layer, resulting in a significant drag reduction of 36.6%. The multi-port injector array film cooling also effectively distributes the low skin-friction resistance region due to the low molecular viscosity after the secondary cooling flow injection. Moreover, under supersonic mainstream conditions, the mixing efficiency of the multi-port injector array film cooling structure and the slot injector film cooling structure both decreases, and the difference gradually decreases.