Carbon nanotube (CNT)-doped liquid crystals (LCs) have attracted intensive research studies as prospective materials in optic display devices, microfluidic sensors, and lubricants due to their unique molecular structures and properties. In this paper, the interaction between the doped CNTs and the hosting 4-cyano-4-pentylbiphenyl (5CB) molecules (in both nematic and isotropic phases) was investigated and we focused on the boundary layer rheological properties of the CNT-doped 5CB under external electric field. The experiments were performed by using a quartz crystal microbalance (for boundary layer viscosity investigation) and a rheometer (for bulk viscosity measurement). The results indicate that the bulk viscosity of the CNT-doped 5CB presents an obvious electroviscous effect in its nematic phase while no electroviscous effect in its isotropic phase. Additionally, we found that the boundary layer viscosity of the CNT-doped 5CB demonstrated significant electroviscous effects both in its nematic phase and isotropic phase. The enhanced electroviscous effects on the boundary layer viscosity of CNT-doped 5CB can be attributed to the highly ordered structures of LC molecules and CNTs on the substrate under external electric field. The unique properties of the boundary layer rheology of CNT-doped 5CB LC were further discussed in view of the ordering of LC molecules induced by the electric field, the polarity of CNTs, and the aligning interaction between CNTs and LC molecules.