For chip-to-chip interconnection, a Pbit/s-class transmission capacity is expected to be developed in near future. To achieve such a huge capacity, a multilayer optical waveguide structure for connection between chips is indispensable. In this paper, a square base cuboid-core structure with size modulation for vertical light beam propagation in a polymer multilayer waveguide is proposed for improving optical coupling between the optical devices and waveguide. A 10-layer polymer waveguide with nonuniform cuboid cores are designed for single-mode transmission at 1.31 μm. Using a simulation based on the beam propagation method, it is confirmed that the proposed design can provide a coupling efficiency of −4.4 dB, which is 3.8 dB higher than that of a previously reported uniform cube-core design, for the 10-layer structure and a crosstalk of −20.6 dB. The simulated results show that the proposed nonuniform cuboid-core structure has the potential to realize a 10-layer optical waveguide structure for future chip-to-chip optical interconnection with a huge transmission capacity.