We have synthesized iron oxide-containing mesoporous silica MCM-41 by a direct route. This material has a significant microporousity, which might be related with the loading of iron oxide in the MCM-41 mesopores, though no crystalline phases of iron oxide were detected by XRD. Intensity deviations and extra bright intensity within the pores, as well as local superstructural phases within a large area, were observed in the TEM images. The position and area of such a crystalline phase could change during the successive electron beam exposure and resulted in a formation of a cycle. These phenomena imply the possible existence of small Fe2O3 nanocrystals loaded in the mesoporous silica materials with regular and oriented arrangement. EELS spectrum of the smaple proves the existence of iron, but the chemical environment of iron in the MCM-41 silica should be different from that of bulk amorphous porous iron oxide. The small iron oxide crystals in the MCM-41 sample might be linked with silica wall through oxygen. Another possibility is that iron oxide reacts with silica during synthesis, causing the partial crystallization of the MCM-41 framework. In other words, microcrystals of iron oxide may exist in the silica matrix.