Abstract Hydrogen two-stage direct-injection enrichment is a novel injection strategy to utilize hydrogen more efficiently and effectively in gasoline rotary engines by inheriting the merits of hydrogen and direct injection simultaneously, such as flexible control, efficiency improvement, and emissions reduction. Based on the CONVERGE code with detailed chemistry solvers, a full-cycle CFD modeling including hydrogen jet-flow and combustion processes was presented and validated by experimental data. To understand the role of hydrogen two-stage injection in improving engine performance at part-load and lean-burn regime, six different injection arrangements for which two-stage injection strategies with variable hydrogen amount for each pulse (up to 30% for post-injection) had considered. The different effects on species evolution, combustion characteristics, knock propensity, and emissions formation were analyzed step-by-step. The simulation results showed that compared with direct-injected hydrogen for single-pulse, injecting adequate hydrogen in the second pulse after spark-ignition onwards performed a significant beneficial effect on the mixture stratification and flame propagation, especially for the trailing part of the rotor chamber, which contributed to the improvement in both combustion characteristics and thermal efficiency. The assessment of knock propensity demonstrated that the two-stage direct-injected hydrogen had the potential of mitigating the knock under lean operations. Using split injection accompanied by an optimized hydrogen allocation strategy allowed substantial unburned hydrocarbon and carbon monoxide reductions with a slight nitrogen oxide penalty rate due to the elevated combustion temperature.