Orientation of the lamellar microdomains in thin films of three symmetric polystyrene-b-poly(ethylene-co-butylene) block copolymers (S65E155, S156E358, and S199E452) on mica was investigated via atomic force microscopy (AFM), grazing incidence X-ray diffraction (GIXRD) and X-ray photoelectron spectroscopy (XPS). The results show that lamellar orientation in the SxEy block copolymers greatly depends on the molar mass of the block copolymers, the temperature of solvent evaporation, and annealing. The nascent thin film of the low molar mass block copolymer, S65E155, shows a multilayered structure parallel to the mica surface with the PS block at both polymer/mica and polymer/air interfaces, but the high molar mass block copolymers, S156E358 and S199E452, exhibit a structure with lamellar microdomains perpendicular to the mica surface. When the solvent is evaporated at a lower temperature, the crystallization rate is fast and a two-dimensional spherulite structure with the lamellar microdomains perpendicular to the mica surface is observed. Annealing of all the thin films with lamellar microdomains perpendicular to the mica surface leads to morphological transformation into a multilayered structure parallel to the mica surface. In all SxEy thin films on mica, the stems of PE crystals are always perpendicular to the interface between the lamellar PE and PS microdomains. A mechanism is proposed for the formation of different microdomain orientations in the thin films of semicrystalline block copolymers. When the thin film is prepared from a homogeneous solution, microdomains perpendicular to the substrate surface are formed rapidly for strongly segregated block copolymers or at a lower crystallization temperature and kinetically trapped by the strong segregation strength or solidification of crystallization, while for weakly segregated block copolymers or at slower crystallization rate, the orientation of the microdomains is dominated by surface selectivity.