An apparatus and method for a large-scale high-throughput quantitative characterization and three-dimensional reconstruction of a material structure. The apparatus having a glow discharge sputtering unit, a sample transfer device, a scanning electron microscope unit and a GPU computer workstation. The glow discharge sputtering unit can achieve large size (cm order), nearly flat and fast sample preparation, and controllable achieve layer-by-layer ablation preparation along the depth direction of the sample surface; rapid scanning electron microscopy (SEM) can achieve large-scale and high-throughput acquisition of sample characteristic maps. The sample transfer device is responsible for transferring the sample between the glow discharge sputtering source and the scanning electron microscope in an accurately positioning manner. The GPU computer workstation performs splicing, processing, recognition and quantitative distribution characterization on the acquired sample characteristic maps, and carries out three-dimensional reconstruction of the structure of the sample prepared by layer-by-layer sputtering.