In the practical application of indoor visible light positioning technology, the signal-to-noise ratio is reduced to some extent because of the effect of the ambient light. This is a challenge to the visible light positioning system based on the received signal strength. A visible three-dimensional positioning system based on sub-carrier modulation is studied. The interference of the ambient light on signals is decreased using sub-carrier frequency selection in the receiver. The identity information and received signal strength of LED is obtained by noncoherent demodulation. The target's location is computed based on an bare-bones particle swarm optimization algorithm. The three-dimensional positioning tests under different intensities of ambient light and different heights are carried out in a space of 1 m×1 m×1.89 m. The results show that the average three-dimensional positioning error of all test points is around 3.00cm, and the positioning errors are 2.83, 2.98 and 2.83 cm respectively when the height is 0.21 m and the illuminations of ambient light are 0, 10 and 30 lx. Experiment shows that the visible light positioning system based on subcarrier modulation can effectively reduce the positioning error caused by ambient light.