The multi-angle total internal reflection fluorescence microscopy tomography imaging technology is one of the main techniques for achieving the axial super resolution. The key algorithm is to solve the inverse problem based on the alternating direction multiplier algorithm. In order to further improve the iterative speed and convergence of the alternating direction multiplier algorithm, we propose an improved alternating direction multiplier algorithm based on relaxation factors, which is used for the solution of the inverse problems and whose core idea is to solve the relaxation process of the Lagrangian function decomposition iterative process. Based on the proposed algorithm, the multi-angle total internal reflection fluorescence microscopy imaging system is built. The image stacks with different penetration depths corresponding to different illumination angles are acquired. Then the depth information of cell microtubules is reconstructed using the improved algorithm, and the axial resolution of the system is also given. Moreover, the convergence speed comparison of the improved algorithm with the traditional alternating direction multiplier algorithm is accomplished and the range of relaxation factors for the improved algorithm to achieve the optimal convergence is also given. Finally, the three-dimensional information of mitochondrial samples is reconstructed by long time photographing, and the consecutive processes of fusion and fission are observed. The experimental results show that the improved alternating direction multiplier algorithm can be used to achieve an axial resolution of 40 nm. Moreover, the convergence speed of the iterative process is improved by more than 20% when the image reconstruction quality is ensured.