The structural transformation of WO3/SiO2 caused by thermal treatment was characterized by different techniques (X-ray diffraction (XRD), Raman and X-ray photoelectron spectroscopy (XPS)) and its effect on the catalytic performance in selective cyclopentene oxidation to glutaraldehyde was investigated. When calcined at ca. 673 K, the WO3 was present in the Keggin-type structure on the silica surface. With the further increase in calcination temperature, partial collapse occurred and the distorted structure coexisted with crystallite WO3. The correlation of the activity to structural feature was studied, which clearly demonstrated that the species resulted from the partial decomposition of Keggin-type structure, rather than crystalline WO3 species were involved in the catalysis.