Various embodiments of a compensated photonic device structure and fabrication method thereof are described herein. In one aspect, a photonic device may include a substrate and a functional layer disposed on the substrate. The substrate may be made of a first material and the functional layer may be made of a second material that is different from the first material. The photonic device may also include a compensation region formed at an interface region between the substrate and the functional layer. The compensation region may be doped with compensation dopants such that a first carrier concentration around the interface region of function layer is reduced and a second carrier concentration in a bulk region of functional layer is reduced.