A novel spot-size converter (SSC) incorporating phase matched polycrystalline-silicon (Poly-Si) multi-layer is proposed and optimised for efficient nanophotonic coupling, which can be fabricated by using the CMOS compatible process and can be directly integrated. An efficient algorithm, combining the rigorous H-field based full-vectorial finite element method and the least squares boundary residual method, is developed for the design optimization of the SSC. Use of simple single layer and multi-layer Poly-Si based SSCs are investigated, in which the coupling process, phase matching for isolated and composite waveguides are also carried out. The coupling loss can be reduced to 2.72 dB by using an eleven Poly-Si layers based SSC. The on-chip integrated SSC opens up the feasibility of a low cost passive aligned fiber-pigtailed electronic-photonics integrated circuits platform.