The effects of wall surface features on the rheological properties and phase orientation of liquid crystalline polymer (LCP) melts flowing in a nanochannel have been first investigated by molecular dynamics (MD) simulations. The surfaces are modeled as rough atomic serrated walls whereby the roughness is characterized by the period and amplitude of serration. The molecular chains of LCPs are depicted by a newly developed molecular model named the GB-spring-bead model. Through simulating the phase formation of LCP melts, the new model was evaluated and the results have shown the new model is efficient and accurate to describe semi-flexible main-chain LCP molecules. MD simulations of the effect of wall surface features on the LCP shear flow were conducted and the results have revealed the surface features affect greatly the rheological properties and phase orientations of LCP melts in a nanochannel (the distance between the upper wall and the lower wall is ). Findings in this study provide very useful information in the injection molding of plastic products with nanofeatures.