The collapse of trees can be mainly attributed to the decay and hollow in standing timber. The internal structure of standing timber is verified to determine the internal defects. In this study, a method is proposed to detect the internal defects in standing timber based on microwave tomography. First, a microwave tomography system comprising 16 antennas is developed. Second, a healthy wood model and two wood models with different defects are simulated at a frequency of 1 GHz. Third, the finite element analysis software is used to simulate the internal electric field characteristics of the standing timber, based on which image reconstruction can be performed using the linear backprojection image reconstruction algorithm, thereby reconstructing the dielectric constant distribution map inside the wood. Then, the reconstructed image is analyzed based on the average structural similarity index. Finally, qualitative and quantitative analyses of the different trunk models and reconstructed image are conducted. Simulation results demonstrate that the position and size of a defect can be directly identified using the proposed microwave tomography system based on the visualization effect of the reconstructed permittivity distribution map.