Directed self-assembly (DSA) of block copolymer (BCP) is a promising and economic method of manufacturing periodic lamellar patterns on wafer that is widely used in semi-conductor and electronic fields. In BCP DSA lithography, same as issues in achieving defective free patterns and smooth edges, an evenly distributed width line space pattern is also critical but in lack of research. Comparing with experiment, simulation has many advantages on cost, accuracy and repeatability. Simulation has been very successful in predicting physical behaviors of systems and guiding the experiments. In this research, a coarse grained molecular dynamic (CGMD) simulation on polystyrene-b-poly (methyl methacrylate) (PS-b-PMMA) block copolymer DSA process using chemoepitaxial method was carried out. By changing BCP composition, substrate properties including topography and interaction strength, their effects on produced lamellae critical dimension (CD) variation, line space variation, roughness and tapering effect were investigated. It gives the direction of optimizing the substrate structure.