The rheological properties and phase orientation of liquid crystalline polymer (LCP) melts flowing in a nanochannel with different surface roughness are investigated by molecular dynamics (MD) simulations. Simulation results show the surface roughness has great impact on the rheological properties and phase orientation of LCP melts in the nanochannel (cross section is 12nm). As the amplitude of serrations increases, the shear viscosity increases nonlinearly and the value of orientational order parameter decreases. When the serration amplitude is larger than 1.1nm, a phase transition (from nematic to isotropic phase) of LCP melt happens, which makes flowing in nanochannels more difficult. On the other hand, the influence of serration period on the shear viscosity and orientational order parameter are found not so obvious. Findings in this study will be helpful for injection molding plastic products with nanofeatures.