We report a template route to modify MoO3 molecules with FexOy by using metal-complex of Fe-phenanthroline (Fe-phen) as template. Fe-phen complex self-assembled with polyoxomolybdate into a Fe-phen/polyoxomolybdate hybrid easily and this hybrid decomposed into FeOOH/MoO3 nanocomposite after calcinations. Single crystalline MoO3 nanoparticles have been obtained with FeOOH doped in it. By this method the semiconductor MoO3 molecules have been successfully modified with FexOy. This research makes it possible to prepare magnetic-semiconductor nanomaterial by using metal-ligand complex as template via in situ self-assembly route very easily in future and also supplies new techniques to prepare organic-inorganic hybrid materials via a green and efficient way. Crown Copyright (c) 2012 Published by Elsevier Ltd. All rights reserved.