Jet Controlled Compression Ignition (JCCI) mode with dual-direct injection of diesel and gasoline has been demonstrated by the engine experiments to provide an effective control on the combustion process without sacrificing the advantages on efficiency and emissions performance. The multiple-objective optimization of JCCI mode based on the 186FA engine at 75 % engine load with an engine speed of 3000 r/min was carried out in this research by the combination of Three-Dimensional (3D) Computational Fluid Dynamics (CFD) and Genetic Algorithm (GA). The simulation results indicate that the ignition timing and the combustion phasing can be effectively controlled by the jet-injection diesel, and the pre-injection gasoline mainly affects the combustion stage from CA50 to CA90. With the increase of the pre-injection energy ratio, higher initial in-cylinder temperature is required to ensure the engine performance. The optimal results present that JCCI mode can achieve high efficiency and low emissions simultaneously when the combustion phasing is at 5 ∼ 9 °CA ATDC. The low EISFC, NOx and soot emissions can be realized when SOIpre and SOIjet are retarded to −63 and −28 °CA ATDC, respectively, which prepares the appropriate premixed charge considering the equivalence ratio and reactivity. The comparisons of the typical cases reveal that the high-temperature combustion process gradually translates to the two-stage characteristics when the SOIjet retards from −27.77 to −18.88 °CA ATDC, the combustion duration is prolonged slightly and the in-cylinder temperature is decreased, resulting in the reduction of pmax by 0.42 MPa, NOx emissions by 0.07 g/kWh, associating with the lower heat transfer loss and exhaust loss. In addition, the NOx emissions in JCCI mode are mainly generated within the high-temperature combustion region of the jet-injection diesel spray target location.