In order to realize the coupling and steering of polysiloxane polymer optical waveguides with a cross-sectional dimension of 50 μm×50 μm, a multilayer etched grating coupler with high refractive index cladding was designed. Firstly, the structural factors affecting coupling efficiency of polymer waveguide grating couplers were analyzed. Then, the coupling efficiency of polymer waveguide grating coupler was improved by etching the high refractive index layer on the grating surface. Next, different grating structures were formed by arranging and combining different periods (range: 100-4 000 nm) and different etching depths (range: 0-50 000 nm), where all cases were traversed to obtain the diffraction field distribution and its coupling efficiency of different grating structure based on finite-difference time-domain (FDTD) method. Beyond that, the optimization of period and etch depth were found to maximize coupling efficiency. Finally, a multilayer etched grating coupler was designed to further improve the coupling efficiency. The coupling efficiency of the uniform grating coupler with high refractive index layer was approximately 17.2% with 5 000 nm etching depth and the 2 600 nm grating period. The coupling efficiency is approximately 37.4% with multilayer etching and optimized structure. It provides a theoretical reference for the practical application of polysiloxane polymer optical waveguide in optical interconnection.