This paper reports a novel approach to modify a microfluidic chip by hybrid molding of small pieces to the inner wall of PDMS microchannel exposing the surface of the pieces. In this research, we employed a LSI chip and a microfabricated chip as an embedded piece. Addition of intermediate material between a piece to be embedded and a mold prevent a functional surface of the piece from possible coverage with PDMS. Agarose gel showed the best performance as such intermediate material. The use of the optimal amount of agarose successfully embedded a bare LSI chip as a functional piece into the inner wall of PDMS microchannel without wraparound or moat. This research enables us to fabricate microfluidic chips of complicated hybrid structure with various sensors as chip at low cost.