As a zero-carbon fuel, the characterization of hydrogen in the combustion process has become a hotspot in the development of advanced engine technology. This paper analyzes the numerical simulation method for hydrogen super-combustion characteristics and designs the control equation for hydrogen combustion. On this basis, the gas-phase model and particle-phase model are constructed, and the numerical simulation experiment based on hydrogen combustion characteristics is carried out by combining the graph theory analysis algorithm. In this paper, the absolute values of the difference between the mixing efficiency and total pressure loss measured in the combustion chamber of the DLR scramjet engine and the Kummitha model are between 0.001 and 0.04, and the results are close to each other. The temperature distribution in the high-temperature region of the combustion chamber was between 400 K and 2000 K at fuel hydrogen doping ratios of 0 to 0.3, and the axial maximum temperature increased with the increase of hydrogen doping ratio. With the increase in the combustion chamber temperature, the CO emission from carbon particles showed a decreasing trend with a decrease of 5.32% to 7.51%. In addition, the increase in hydrogen doping of the fuel increased the blowout limit of the combustion flame, while the flame quenching limit was the opposite. This paper provides recent advances in the numerical simulation of hydrogen supersonic combustion characteristics through the application of graph theory algorithms to combustion dynamics.