In this study, multi-objective optimizations of a reactivity controlled compression ignition engine are performed. The main focus is the investigation of effects of seven design variables, including swirl ratio, the first and second start of injections (SOI1 and SOI2), and four injection rate-shape parameters, on the objective parameters, namely, gross indicated efficiency, the second-law efficiency, ringing intensity, and emissions. The results show that in the low swirl ratio range (swirl ratio < 1), the emissions decrease by either increasing boot length or decreasing boot velocity. The physical analysis reveals that this is due to the penetration of the high-reactivity fuel vapor in whole squish area and a large portion of the crevice. This is because the more uniform mixture in the squish region slightly mitigates the formation of hot spots and NOx, and the propagation of reaction deeper into the crevice considerably reduces carbon monoxide and unburned hydrocarbons there. The sensitivity analysis manifests that swirl ratio has the strongest effect on all objectives, and besides swirl ratio, SOI2 has the greatest impact on gross indicated efficiency and emission, while SOI1 has the strongest influence on second-law efficiency and ringing intensity. The optimal case with an advance of SOI1 and a slight retard of SOI2, that is, a longer duration between the two injections, a lower swirl ratio (of 0.5) with respect to the base case, and appropriate injection rate-shape parameters (a high boot length and low boot velocity), achieves the gross indicated efficiency of 54% and merit function of 615.