The invention relates to the technical field of semiconductors, and provides a compound semiconductor silicon-based mixer device and a preparation method thereof. The preparation method comprises thesteps of sequentially forming a sacrificial layer and a semiconductor function layer on a first substrate to form a first component, dividing a second substrate into an optical waveguide region and abonding region, forming an optical waveguide structure on the optical waveguide region, forming an alignment assembly in the bonding region, forming a bonding boss on the surface of the bonding region; arranging a first component on the bonding region, wherein the semiconductor function layer is bonded with the bonding boss, and the side wall, close to the optical waveguide region, of the semiconductor function layer is coupled with the end surface of the optical waveguide structure. According to the method, the problem of accurate alignment (namely passive alignment in the vertical directionand the horizontal direction) of the semiconductor function layer and the optical waveguide structure can be avoided. In addition, the integration degree of the semiconductor device and the coupling degree of the compound semiconductor photoelectric device and a silicon-based optical waveguide are improved, and the production efficiency is improved.