An silicon photonics device of hybrid waveguides having a coupling interlayer with an accurately controlled thickness and a method of making the same. The device includes a first plurality of Si waveguides formed in a SOI substrate and a first layer of SiO2 overlying the first plurality of Si waveguides and a second plurality of Si3N4 waveguides formed on the first layer of SiO2. At least one Si3N4 waveguide is disposed partially overlapping with at least one of the first plurality Si waveguides in vertical direction separated by the first layer of SiO2 with a thickness controlled no greater than 90 nm. The device includes a second layer of SiO2 overlying the second plurality of Si3N4 waveguides. The method of accurately controlling the coupling interlayer SiO2 thickness includes a multilayer SiO2/Si3N4/SiO2 hard mask process for SiO2 etching and polishing as stopping and buffering layer as well as Si waveguide etching mask.