The coordination structures of vanadium and iron introduced into MCM-41, a typical mesoporous silica, by both direct hydrothermal synthesis (DHT) and templateion exchange (TIE) methods have been studied by X-ray absorption spectroscopy (XANES and EXAFS). Vanadium is tetrahedrally coordinated with oxygen in V-MCM-41 prepared by both methods but the location of vanadium is probably different; vanadium is mainly incorporated inside the framework of MCM-41 by the DHT method as the content is lower than approximately 1wt%, while the vanadyl tetrahedra are probably dispersed on the wall surface of MCM-41 over the samples by the TIE method. In the case of Fe-MCM-41, the DHT method results in iron atoms mainly in tetrahedral coordination and isolated from each other in the framework of MCM-41. However, aggregated iron oxides with iron in octahedral coordination are mainly observed in the TIE samples. The V-MCM-41 by the TIE method shows better catalytic performances than that by the DHT method in the partial oxidation of methane to formaldehyde with oxygen. However, the Fe-MCM-41 by the DHT method exhibits remarkably higher methane conversion and formaldehyde selectivity than that by the TIE method.