Mixing between two or more reagents is one of important processes in biochemical microfluidics. In efficient micromixer design, it is essential to analyze flow pattern and evaluate mixing efficiency with good precision. In this work, mixing efficiency for Y-channel micromixer is measured by fluorescence intensity using LIF(Laser Induced Fluorescence) Confocal Microscope. The Y-channel micromixers are fabricated with polydimethylsiloxane(PDMS) and those are bonded to glass plate through Plasma bonding. Nile Blue A is injected into the micromixer as a fluorescence dye for measuring of fluorescence intensity by He/Ne laser. For visualization of the flow pattern, dynamic image capturing is carried out using CAM scope. For the comparison with computer simulation, modified SIMPLE algorithm for incompressible flow equation is solved for the same geometry as in the experiment. Throughout the experiments and computer simulation, accurate mixing efficiency evaluation process for a PDMS Y-channel micromixer is established.