In the field of integrated circuits, electron beam images can provide process parameter information such as linewidth and line spacing. However, this size information only accounts for a small proportion of the information that the image can provide. To maximize the information obtained from electron beam images, this paper proposes a three-dimensional reconstruction method based on the electron beam imaging model. This method reveals the relationship between the top-view scanning electron microscopy (SEM) image and the actual three-dimensional structure. And then, an iterative optimization method is used to optimize the model and structure parameters for 3D reconstructions. During optimization flow, the correlation between the real SEM image and the reconstructed image is used to build the cost function. Two-micrometer silicon structures, vertical edge, and rounded sidewall structures are applied to model verification. Results show that the proposed model, with a fitting correlation over 99.3% and edge-angle mismatch within 1°, does well in rebuilding both structures. Our method makes it possible for high-precision 3D profile metrology and defect inspection.