In view of the disadvantages of the indoor visible light three-dimensional positioning system, such as complex calculation and low precision, we propose an indoor visible high precision three-dimensional positioning system based on immune algorithm. The immune algorithm, which is designed according to the biological immune system, is an intelligent algorithm with global optimization ability. The immune algorithm can be used to solve the global optimization problem. In the visible light communication (VLC)-based indoor positioning, it can be transformed into a global optimization problem. Therefore, in the three-dimensional indoor positioning, the best receiver coordinates can be obtained through the immune algorithm. However, owing to the system noise and the imperfection of device used in the system, distance between receiver and transmitters deviates from the real value, and results in positioning error. By introducing the error correction factors into the immune algorithm, we can precisely determine the coordinates of the receiver in three-dimensional space. The simulation result shows that the average distance error is 0.69 cm within 80 iterations in an indoor environment of 3 m×3 m×4 m. The average positioning error of the multi-point positioning test is 2.13 cm. The extended experiment in motion scene positioning also shows that 96.04% positioning errors of the proposed method are below 1.7 cm, which is superior to that of other existing methods for three-dimensional visible light indoor positioning. Therefore, the indoor visible three-dimensional positioning system based on the immune algorithm can achieve high-precision positioning services, and have potential application in various indoor positioning scenes.