In this study, we report a neo-conceptive three-dimensionally (3D) crossing manifold micromixer (CMM) embedded in microchannel. Fabricated by sequential processes of photolithography and two photon absorption stereolithography, this leads to a microfluidic system with a built-in micromixer in a site controlled manner. The effectiveness of CMM is investigated numerically and experimentally. Through the numerical simulation, it is estimated that a high mixing ratio of 90% can be obtained even in a channel length shorter than five times the channel width. This compares well with the conventional passive type of micromixers that have a gradual increase in mixing efficiency with the length of the channel. Furthermore, the mixing performance of the realized CMM built-in microchannel is observed by confocal microscopy.