Water injection for absorbing corrosive gases NH3, HCl and H2S is a widely employed method to mitigate the risk of ammonium salt corrosion in the hydrogenation units. To ensure the efficient prevention of ammonium salt corrosion, a numerical model integrating the hydrodynamics of gas–liquid and the reaction of interphase mass transfer was built based on Euler–Lagrange method in this work. The flow and mass transfer characteristics of complex multi-component system in water injection pipeline were investigated, and the correlation between process operating conditions and gas removal performance was analyzed. The results reveal that the removal efficiencies of corrosive gases in pipeline are influenced by the characteristics of gas–liquid flow and mass transfer, with HCl showing higher removal efficiency compared to NH3 and H2S. Furthermore, the increasing flow rate of water injection, the reducing corrosive medium content and the decreasing droplet diameter have a positive impact on the removal efficiencies of corrosive gases, while the impact of gas-flow velocity on the removal efficiencies of corrosive gases primarily depends on the residence time of droplets. These results have important theoretical value and engineering guiding significance for intensifying the process of water injection in hydrogenation units.