High-pressure direct-injection (HPDI) natural gas marine engines are widely used because of their higher thermal efficiency and lower emissions. The effects of different injection rate shapes on the combustion and emission characteristics were studied to explore the appropriate gas injection rate shapes for a low-speed HPDI natural gas marine engine. A single-cylinder model was established and the CFD model was validated against experimental data from the literature; then, the combustion and emission characteristics of five different injection rate shapes were analyzed. The results showed that the peak values of in-cylinder pressure and heat release rate profiles of the triangle shape were highest due to the highest maximum injection rate, which occurred in a phase close to the top dead center. The shorter combustion duration of the triangle shape led to higher indicated mean effective pressure (IMEP) and NOx emissions compared with other shapes. The higher initial injection rates of the rectangle and slope shapes had a negative effect on the ignition delay periods of pilot fuel, which resulted in lower in-cylinder temperature and NOx emissions. However, due to the lower in-cylinder temperature, the engine power output was also lower. Otherwise, soot, unburned hydrocarbon (UHC), and CO emissions and indicated specific fuel consumption (ISFC) increased for both rectangle and slope shapes. The trapezoid and wedge shapes achieved a good balance between fuel consumption and emissions.