In this study, the combustion and emission characteristics of a diesel/methanol/n-butanol blended fuel engine with different pre-injection timings and pre-injection mass ratios were investigated by a computational fluid dynamics (CFD) model. The CFD model was verified by the measured results and coupled with a simplified chemical kinetics mechanism. Firstly, the corresponding three-dimensional CFD model was established by CONVERGE software and the CHEKMIN program, and a chemical kinetic mechanism containing 359 reactions and 77 species was developed. Secondly, the combustion and emission characteristics of the diesel engine with different diesel/methanol/n-butanol blended fuels were analyzed and discussed. The results showed that increases in the pre-injection timing and the pre-injection mass ratio could increase cylinder pressure and cylinder temperature and decrease soot, HC, and CO emissions. At 100% load, the maximum cylinder pressures at the start of pre-injection timing from −15 °CA to −45 °CA, were 7.71, 9.46, 9.85, 9.912, and 9.95 MPa, respectively. The maximum cylinder pressures at pre-injection fuel mass ratios from 0.1 to 0.9 were 7.98, 9.10, 9.96, 10.52, and 11.16 MPa, respectively. At 50% load, with increases of the pre-injection timing and pre-injection fuel mass ratio, the soot emission decreased by 7.30%, 9.45%, 27.70%, 66.80%, 81.80% and 11.30%, 20.03%, 71.32%, 83.80%, 93.76%, respectively, and CO emissions were reduced by 5.77%, 12.31%, 22.73%, 53.59%, 63.22% and 8.29%, 43.97%, 53.59%, 58.86%, 61.18%, respectively. However, with increases of the pre-injection timing and pre-injection mass ratio, NOx emission increased. In addition, it was found that the optimal pre-injection timing and optimal pre-injection mass ratio should be −30 °CA and 0.5, respectively. Therefore, through this study we can better understand the potential interaction of relevant parameters and propose pre-injection solutions to improve combustion and emission characteristics.