Abstract: In order to simulate the underground modified root of crops visually, taking fleshy tap root and tuberous root as the simulation objects, the point clouds of modified root were got with three-dimensional reconstruction method based on voxel coloring, and the preprocessing pipeline for filling the holes and eliminating acoustical noise and outlier in point clouds was put forward and implemented. The surface reconstruction was finished on the basis of point clouds that had been preprocessed. The architectural parameter of modified root was extracted from the reconstructed mesh model, and then the visual simulation of the reconstructed mesh was implemented. Carrot and potato were taken as the experimental subjects for visual simulation. The results indicate that the integral, uniform distributed and smooth point clouds model can be obtained by the preprocessing pipeline with the function of eliminating the noise and outlier in point clouds, and filling the holes. Error of volume extracted from the mesh model is less than 10%. The shape of the modified root can be visualized smoothly and vividly with the mesh model from surface reconstruction. The study can provide a new method for the research on simulating the plant modified root.