The effect of pressure on the structure, interionic interactions, and properties of the ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF(6)]) was studied using an all-atom molecular dynamics simulation. A distinct conformational transition from anti (a) to gauche (g) form based on the deformation of the first C-C bond of the butyl chain was observed under high pressure, and the ratio of the a conformation that changed into the g conformation was 5.5% at 6000 bar. Under high pressure, the configuration of the a and g conformer for [C(4)mim](+) tends to make the alkyl chain distorted to the inside of the ring. Results on the density changes indicate a small increase from 5000 to 6000 bar, which could be attributed to the writhing of the reducing end of the alkyl chain in the cation at higher pressure. These simulation results are well agreed with the experimental results. Transport properties were also calculated at different pressures. The results show that diffusion of the ions is reduced under high pressure, and the viscosity is dramatically enhanced.