A semiconductor structure and a manufacturing method thereof is provided. The semiconductor structure includes a high-resistance silicon substrate and a compound layer located on the high-resistance silicon substrate, by performing a way such as local n-type ion implantation, local n-type ion diffusion, selective region epitaxy growth and the like to the high-resistance silicon substrate, an upper part of the high-resistance silicon substrate is formed into a plurality of local n-type semiconductor regions, p-type semiconductor conductive regions formed in the upper part of the high-resistance silicon substrate due to a diffusion of Al, Ga atoms in the compound layer are eliminated, thereby parasitic capacitance caused by a conductive substrate is greatly reduced, and a resistivity of the high-resistance silicon substrate may be improved under high temperature conditions, and then efficiencies and radio frequency characteristics of a microwave device constituted by the entire semiconductor structure are improved.