A three dimensional polymer waveguide with taper structure was demonstrated and fabricated by a reliable and effective hybrid lithography. The hybrid lithography consists of lithography to fabricate a polymer waveguide and gray scale lithography to fabricate a polymer taper structure. Laser ablation and shadow aluminum evaporation were designed for gray scale lithography. The length of the gray scale region ranging from 20 to 400 μm could be controlled by the laser power, the ablation speed, and the aluminum thickness. The slope angle was determined by the length of the gray scale region and the thickness of the photoresist. The waveguide taper structure could be transferred to the lower layer by the etching method. The taper structure can be used for integration of the waveguide with different dimensions.