The structure of MnxSi1-x magnetic semiconductor thin films prepared by molecular beam epitaxy(MBE) on Si(100) substrate at 600 ℃ has been studied by X-ray diffraction (XRD) and X-ray absorption near edge structure (XANES) technique. The XRD results show that in the MnxSi1-x thin films with high Mn doping concentrations (x=0.08 and 0.17), only diffraction peaks of crystalline Mn4Si7 are observed. XANES results indicate that all the Mn K-edge XANES spectra of MnxSi1-x thin films with different Mn doping concentrations (x=0.007, 0.03, 0.08 and 0.17) show the similar feature. XANES calculation based on multiple-scattering theory further reveals that the experimental spectra for samples with different Mn doping concentrations are reproduced by the calculated Mn4Si7 spectrum. These results reveal that for the MnxSi1-x magnetic semiconductor thin films, Mn atoms mainly exist in the Si thin film substrate in the form of Mn4Si7 nanocrystalline grains, the substitutional or interstitial Mn atoms scarcely exist.