We investigated the microscopic strain fluctuation in strained-Si grown on SiGe-on-insulator (SGOI) and SiGe virtual substrates, and clarified the origins of the strain fluctuation in the strained-Si film. A periodic strain fluctuation, which reflects a cross-hatch pattern of the substrate, was observed in the sample on the virtual substrate. On the other hand, a featureless strain fluctuation with suppressed amplitude was observed in the sample on SGOI substrate. By analyzing the correlation of the Raman peak positions of the Si–Si modes in strained-Si and SiGe, the dominant mechanism of the strain fluctuation in the strained Si film was found to be the compositional fluctuation in underlying SiGe for the sample on SGOI, and the strain fluctuation reflecting the cross-hatch pattern for the sample on the virtual substrate, respectively.