Correctly identifying and describing the position and structure of the internal wood defects, such as internal decay, knots, dry rot, etc., is significant for old tree conservation, urban tree and commercial wood assessment, and mending of cultural relics. This study was performed to simulate the three-dimensional (3D) structure of the tree's internal decay based on the data obtained by ultrasound technique. The original data of internal decay were obtained at different tree height positions using TRU Tree Radar, and then they were processed and interpolated in MATLAB software. Two methods simulated the 3D structure of the internal decay, namely surface rendering, and volume rendering. The results showed that the surface rendering method quickly simulated the 3D structure of the tree's internal decay, but the information was incomplete and less intuitive. The volume rendering method can accurately simulate the complex structures of internal decay. The study successfully experimented with and proposed parameter values adjustment of the grayscale linearization algorithm to improve the visualization of the tree’s internal decay simulation structure. A graphical user interface was designed for image visualization of lesions and defects inside the tree trunk or wood.