The acidic components in vacuum gas oil (VGO) of cut-2, cut-3, and cut-4 and their corresponding dewaxed oils from a refinery were characterized by negative-ion electrospray ionization (ESI) Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The acidic heteroatom compounds, N-1, N-2, N1O1, N1O2, O-1, and O-2 class species, were identified. Among them, the abundance of O-2, O-1, and N-1 class species were much higher than other acidic class species and characterized by double-bond equivalent (DBE) values and carbon numbers. The N-1, N-2, N1O1, and N1O2 classes were only identified in VGO cuts instead of dewaxed VGOs. The composition of acidic compounds in VGOs and dewaxed VGOs were correlated with increased boiling point and varied in DBE and carbon numbers. For all identified naphthenic acids, polycyclic naphthenic acids were dominant in VGO cuts, while in their dewaxed oils, naphthenic acids with single-ring were dominant. The most abundant O-1 class species had DBE values of 4 corresponding to alkyl phenols in three VGO cuts as well as in three dewaxed VGOs. The abundant N-1 class species in three VGO fractions were centered at DBE values of 9 and 12, and these species were likely carbazoles and benzocarbazoles, respectively, while the N-1 class species with a DBE of 9 were dominant in three dewaxed VGOs.