Abstract Natural gas is a preferred fuel choice owing to its easy availability, clean combustion, and low emission levels, especially in the field of marine engines. Recently, manifold multi-point gas injection technology was adopted by engine manufactures to improve the response of the marine gas engine to load changes and the consistency of gas fuel supplied to each cylinder. The characteristics of manifold gas injection have a significant influence on the combustion and emissions of marine gas engines. It is therefore vital to investigate the effect of gas nozzle structures on the gas mixture formation and combustion process. In this study, based on the validation through experimental method, a computational fluid dynamics simulation method was adopted to analyze the influence of the nozzle structure on the uniformity of the intake gas mixture in a natural gas engine, and the combustion process was analyzed to show the further effects of nozzle structure on combustion characteristics. The results show that, at high engine load, the structure of the cross multi-hole gas nozzle can help achieve a more homogeneous gas mixture, which is beneficial to the in-cylinder combustion; it yet yields higher NO emission. The single-hole gas nozzle structure yields an inhomogeneous mixture during the intake stroke and has negative effects on combustion. However, at lower engine load, employing a cross multi-hole gas nozzle results in the deposition of gas fuel residue in the intake port during the intake process, thereby inhibiting complete combustion. The structure of the single-hole gas nozzle can provide higher kinetic energy, which has positive effects on fuel intake efficiency and combustion intensity, although there is still an increased NO emission associated with it, owing to a higher cylinder temperature.