The spinodal decomposition of a polymer-polymer-solvent ternary blend spin coated on heterogeneously functionalized substrate is studied in a three-dimensional numerical model. The Cahn-Hilliard equation was used to describe the free energy profile of the domain. The mechanism of the morphology evolution was studied quantitatively. The well-established linear relationship of the characteristic length, R(t), with t(1/3) can be observed in the simulation results. The functionalized substrate greatly affected the morphology evolution of blends with different solvent concentrations. The results indicated that a critical time can be observed, at which the evolution rate changes abruptly, also after which the compatibility of the surface morphology to the functionalized substrate pattern increases at a much lower pace in the diluted solution. In the condensed solution, the compatibility actually decreases beyond the critical time. The influence of solvent evaporation is investigated and a sharper interface was observed in the case with solvent evaporation and film thickness reduction. POLYM. ENG. SO., 50:2329-2339, 2010. (C) 2010 Society of Plastics Engineers