Due to having zero carbon emissions and renewable advantages, hydrogen has great prospects as a renewable form of alternate energy. Engine load and hydrogen substitution rate have a considerable influence on a hydrogen–diesel dual-fuel engine’s efficiency. This experiment’s objective is to study the influence of hydrogen substitution rate on engine combustion and emission under different loads and to study the impact of exhaust gas recirculation (EGR) technology or main injection timing on the engine’s capability under high load and high hydrogen substitution rate. The range of the maximum hydrogen substitution rate was determined under different loads (30%~90%) at 1800 rpm and, then, the effects of the EGR rate (0%~15%) and main injection timing (−8 °CA ATDC~0 °CA ATDC) on the engine performance under 90% high load were studied. The research results show that the larger the load, the smaller the maximum hydrogen substitution rate that can be added to the dual-fuel engine. Under each load, with the increase of the hydrogen substitution rate, the cylinder pressure and the peak heat release rate (HRR) increase, the equivalent brake-specific fuel consumption (BSFCequ) decreases, the thermal efficiency increases, the maximum thermal efficiency is 43.1%, the carbon dioxide (CO2) emission is effectively reduced by 35.2%, and the nitrogen oxide (NOx) emission decreases at medium and low loads, and the maximum increase rate is 20.1% at 90% load. Under high load, with the increase of EGR rate or the delay of main injection timing, the problem of NOx emission increases after hydrogen doping can be effectively solved. As the EGR rate rises from 0% to 15%, the maximum reduction of NOx is 63.1% and, with the delay of main injection timing from −8 °CA ATDC to 0 °CA ATDC, the maximum reduction of NOx is 44.5%.