Optical branch waveguides are one of the most important optical elements and have been widely exploited for optical communication systems. However, prevailing devices are typically solid and have limit in tunability. Liquid optical devices have attracted more interest for the advantage of tunability of liquid media, but their signals suffer serious leakage if the refractive index (RI) of liquid is smaller than that of solid channels. This paper demonstrates the tunable three-dimensional (3D) optofluidic Y-branch waveguides in plannar microchannels by simply introducing Dean flow. This device can reconfigure 3D Y-branch profiles and separate the intensity of light as tunable ratio from 0 to 1 by adjusting the flow rates with low loss. Different from the prevailing 2D liquid counterparts, the 3D configuration offer much more freedom in the selection of liquid media as liquid's RI can be totally independent to the solid channel structure. The transmission loss through the device is estimated to 0.97 db when the splitting angle is 10°, which shows the light is confined better in the 3D liquid structures than traditional 2D liquid counterparts. The Y-branch waveguides show potential in applications of integrated optofluidic devices.