Abstract: In this paper, the algebraic reconstruction algorithm is applied to the newly developed High Energy Electron Radiography(HEER) technology to carry out three-dimensional imaging research, which realizes the accurate diagnosis of the internal structure information of the sample material. The Monte Carlo program and the particle tracking program are used to simulate the high-energy electron imaging process, including the interaction process between the electron beam and the target substance, and obtain the high-energy electron two-dimensional imaging results under the imaging angle of the sample. The ART(Algebraic Reconstruction Technique) algorithm and the Filtered Back Projection (Filtered Back Projection) algorithm were used to simulate experiment of Three-Dimensional High Energy Electron Radiography(TDHEER) respectively, and the three-dimensional images of the sample were reconstructed. These images have been quantitatively compared and analyzed through evaluation indexes. The results show that under the condition that the angle number of projection is 180, the reconstruction results of ART are closer to the original image of the sample, which have higher fidelity and fewer image artifacts. In order to further verify the simulation results, actual experiments were carried out, and the conclusions are the same as the simulation. The results of this study provide a basis for the optimization of the subsequent TDHEER.