A composite structure with an aluminum-based alloy layer containing boron carbide and a manufacturing method thereof are provided. The composite structure includes a substrate with an open hole in that surface and the aluminum-based alloy layer containing boron carbide. The aluminum-based alloy layer is disposed in the open hole and contains aluminum, boron, carbon, and oxygen, wherein the content of aluminum is between 4 at. % and 55 at. %, the content of boron is between 9 at. % and 32 at. %, the content of carbon is between 13 at. % and 32 at. %, the content of oxygen is between 2 at. % and 38 at. %, and the ratio of the content of boron to carbon is between 0.3 and 2.7.