High-pressure methods were applied to investigate the rotational isomerism and the hydrogen-bonding structures of 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Conformation changes of the butyl chain were observed above a pressure of 0.3 GPa. Under ambient pressure, Raman spectra indicate that the more thermodynamically stable butyl structure of the cations is the gauche-anti (GA) and all-anti forms for 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Nevertheless, the high-pressure phases arise from the perturbed GA conformer. The imidazolium C-H bands of 1-butyl-3-methylimidazolium chloride display anomalous nonmonotonic pressure-induced frequency shifts. This discontinuity in the frequency shift is related to the modification of the imidazolium C-H---Cl- contacts upon compression. The alkyl C-H---Cl- interactions are suggested to be a compensatory mechanism to provide additional stability. Density-functional-theory-calculated results also support the high-pressure results that the methyl and butyl C-H groups are suitable proton donor sites for the GA conformer.