The invention discloses a microstructure fiber with fiber core modified by inverse opal (3DOM three dimensional ordered macroporous material). The method mainly comprises the following steps: preparing a PS or PMMA colloid microballoon solution, and adding a predecessor solution (TEOS or TiBALDH) into the colloid microballoon solution in a certain proportion; growing a segment of colloid crystal in a capillary with a Sol-gel cooperation self assembly method, forming predecessor gel when colloid crystal gap moisture is reduced, and sintering the capillary at high temperature in a box-type furnace and removing the colloid crystal to form an inverse opal composition; vertically cutting two common standard fibers after part coating is removed, inserting the two fibers into the capillary from two ends of the capillary to the inverse opal composition, fixing the fibers with glue, and fixing and packaging the capillary and fibers with a thermoplastic cannula. The microstructure fiber prepared in the invention can be used as a fiber filter and a biomedical sensing member. By using a common standard fiber in preparation, the microstructure fiber can connects a present fibre-optical communication network to facilitate the realization of all-optical sensing network. The microstructure fiber has the advantages of simple preparation, reliability and strong versatility.