The structure of MnxGe1-x dilute magnetic semiconductor thin films prepared by magnetron co-sputtering has been studied by X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS) techniques. The XRD results show that in the MnxGe1-x thin film with low Mn doping concentration (x=0.070), only diffraction peaks attributed to crystalline Ge can be observed. In samples with high Mn doping concentrations (x=0.250, 0.360), the secondary phase Ge3Mn5 appears, and its content enhances with Mn doping concentration. The XAFS results indicate that for the Mn0.07Ge0.93 thin film, Mn atoms are mainly incorporated into the Ge lattice and located at the substitutional sites of Ge atoms with the ratio of 75%, while for the Mn0.25Ge0.75 and Mn0.36Ge0.64 samples, most of the Mn atoms are aggregated to form Ge3Mn5.