During the highly transient process of the direct-start in a four-cylinder GDI engine, each cylinder exhibits specific characteristics in terms of in-cylinder conditions and energy demands, necessitating different control for each cylinder. However, recent studies have paid insufficient attention to cylinders other than the first starting cylinder. This paper proposes a comprehensive control strategy based on experimental data from the direct-start process of the second, third, and fourth cylinders, aiming to enhance the characteristics of combustion and emission performance through the optimization of injection timing, equivalence ratio, and ignition timing. The research findings indicate that the second cylinder should inject fuel approximately 10 ms after the first cylinder ignites to mix thoroughly the fuel with air. The ignition timing of the second cylinder should be close to the highest point of the piston movement to minimize hindrance to the piston compression process. The third and fourth cylinders should adopt a delayed injection timing strategy to prevent the escape of injected fuel caused by low engine speed. The optimal ignition timing for the third cylinder is 20 degrees CA BTDC, while the fourth cylinder should be ignited earlier due to its stronger airflow and faster formation of a mixture that can be ignited. As the fuel injection quantity increases, the power output of the three cylinders enhances, but at the same time, emissions also increase. Therefore, their optimal equivalence ratios are determined as 1.2, 1.4, and 1.2, respectively, striking a balance between combustion and emission performances.