A Monte Carlo simulation model of thin film growth based on parallel algorithm is presented. Non-smooth substrate with special defect mode is introduced in such a model. The method of regionalizing is used to divide the substrate into sub-regions. This method is supposed to be modulated according to the defect mode. The effects of surface defect mode and substrate temperature, such as the nucleation ratio and the average island size, are studied through parallel Monte Carlo method. The kinetic process of thin film growth in the defect mode is also discussed. Results show that surface defect mode contributes to crystal nucleation. Analyzing parallel simulation results we find that density defect points, substrate temperature and the number of processors contribute decisively to the parallel efficiency and speedup. According to defect mode we can obtain large grain size more feasibly and the parallel algorithm of this model can guide the non-smooth substrate simulation work. (C) 2011 Elsevier B. V. All rights reserved.