To explore the influence of injection strategy on in-cylinder mixing and combustion, the iterative coupling method was used to study the effects of single hydrogen injection and secondary hydrogen injection in both conventional and linear engines, as well as the influence of different injection ratios on the linear engine. The results showed that the pressure and temperature in the two engines with secondary hydrogen injection were lower than those with single hydrogen injection. For the conventional engine, the pressure and temperature with secondary hydrogen injection were 0.1 MPa and 6.5 K lower than those with single hydrogen injection, while for the linear engine, the pressure and temperature with secondary hydrogen injection were 0.5 MPa and 29.0 K lower than those with single hydrogen injection. The pressure and temperature of the linear engine were lower than those of the conventional engine, with single hydrogen injection being 1.6 MPa and 93.0 K lower, and secondary hydrogen injection being 2.0 MPa and 116.0 K lower. The indicated thermal efficiency of the linear engine was higher than that of the conventional engine, with a difference of 1.5 percentage points for single hydrogen injection and 1.4 percentage points for secondary hydrogen injection. For both the linear engine and the conventional engine, the indicated thermal efficiency of secondary hydrogen injection was higher than that of single hydrogen injection, by 0.5 percentage points for the linear engine and 0.3 percentage points for the conventional engine. As the first hydrogen injection quantity decreased, both the in-cylinder velocity and turbulent kinetic energy of the linear engine gradually decreased until they reached a relatively uniform distribution within the cylinder. There were partial differences in the combustion reaction rate and mixture fraction changes in the cylinder after the top dead center, and the combustion in the cylinder was influenced by factors other than the hydrogen injection strategy.