Microphase-separated structures in poly(styrene-block-isoprene) (SI) block copolymer thin films were investigated by transmission electron microtomography (TEMT). The SI block copolymer showed cylindrical microdomains in the bulk state. Several block copolymer thin films with different thicknesses were prepared by spin-coating and were extensively annealed before the TEMT experiments. Intriguingly, although the cylindrical morphology orienting parallel to the substrate was observed in most of the cases, spherical microdomains were found at certain film thicknesses. The thickness dependence was investigated using a computer simulation based on the self-consistent-field theory, producing a morphological phase diagram based on minimizing free energy. We find that the distortion of the hexagonal lattice of the cylindrical microdomains caused the morphological transition to the spherical microdomains.