We report on the fabrication of ion exchangeable microstructures by femtosecond laser direct writing of an ion exchange photopolymer, poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS). The resultant microstructures are negatively charged in aqueous solution, and can adsorb positively charged species, such as metal ions, nanoparticles, and proteins by electrostatic interaction, forming functional components for chip functionalization. In addition, it is possible to modify the microstructures with positively charged species that make the microstructures sensitive to negatively charged species. As a typical example, a crossed 3D microvessel functionalized with antibodies was fabricated, which reveals great potential for organ-on-a-chip systems. The fabrication of ion exchangeable microstructures holds great promise for flexible chip functionalization.