As an emerging developing technique for next-generation lithography, from self-assembly to directed self-assembly of block copolymer has attracted numerous attentions and has been a potential alternative to supplement the intrinsic limitations of conventional photolithography. In this work, a novel high-χ block copolymer Polystyrene-b-Polytrimethylene Carbonate (PS-b-PTMC) material has been successfully synthesized. It can be directly coated on Si substrates to form periodic micro-phase separation structures by annealing processes without the use of neutral layer or additional top coat. A unique selfassembly surface defect phenomenon called as black and white spots shows two different colors in SEM view. An in-depth study on the phenomenon has been carried out, including experimental characterization analysis, mechanism exploration, process optimization, etc., to find out the internal mechanism leading to the formation of such defects. It is necessary to balance both polymer/substrate and polymer/the free surface interfaces, which could induce the perpendicular orientation of microdomains. On this basis, the mechanism self-assembly defects has been proposed, and then an effective process scheme to remove the defects without affecting the formation of periodic vertical micro-phase separation patterns has also been provided, which showed a great potential of novel block copolymer under the condition of neutral layer free. We also realized the elimination of black and white spots by optimizing the process condition of BCP self-assembly and directed self-assembly (DSA). Valuable information and insights are provided for nanowire patterning in state-of-the-art semiconductor devices.