Reported here is the design and fabrication of three-dimensional (3D) "overpass" microstructures at the junction of crossed microfluidic channels by femtosecond laser direct writing of photopolymers. The post-integrated overpass could be used for guiding different microfluids across the junction without mixing; therefore it is proposed as an enabler for achieving 3D microfluidic chips based on conventional two-dimensional (2D) microchannels. As representative examples, bi-crossed and tri-crossed microchannels have been equipped with bi-connected and tri-connected overpasses, respectively. Flow tests confirm 3D flowing capability. The integration of such overpass structures at the microchannel junction provides an opportunity to impart 3D capability to conventional 2D microchips, thus the method may hold great promise for both functionalization and miniaturization of Lab-on-a-Chip systems.