The invention discloses a multilayer material layered drilling system based on a space combination laser focal point and a drilling method. The drilling system comprises a window opening milling laser, a selective milling laser, a laser beam combiner and a laser focusing and focal point switching module; under the same one drilling optical focusing system, the laser focusing and focal point switching module is provided with the space combination laser focal point; when multiple layers of sheet plates with different materials are machined, the laser focal points with different characteristics can be used for machining the different layers of materials, so that the laser machining efficiency and the laser machining quality can be greatly improved; and in particular, when blind holes of multiple layers of laminated sheet plates with different materials are drilled, and the last layer of laser of the blind holes damage milling of the materials with low threshold, the selective milling laser focal points are used for removing the materials without worrying about damage of the materials with high threshold by the next layer of laser, so that the excellent process stable section is brought, the machining time is saved, the machining efficiency is improved, and the excellent machining effect is obtained.