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Drastically different two-phase microstructures have been reported for alloy epitaxial films, including self-organized nanoscale concentration modulations of vertical and lateral stripes. To understand the disparity of these microstructures, we study their formation mechanisms via spinodal decomposition during film deposition with the aid of computer simulations. Based on the simulation results, a microstructure map is established that describes relationships among the morphology of self-organized two-phase microstructure, initial alloy composition, and deposition rate relative to the phase separation kinetics in the film. Depending on the deposition rate relative to the kinetics of spinodal decomposition in the film, both laterally and vertically modulated microstructures could be obtained.