In order to solve the common problem of clock synchronization between transmitter and receiver in communication system based on time difference of arrival(TDOA), a high accurate indoor visible light positioning algorithm based on double photo detectors(PDs) is proposed in this paper. The algorithm uses three light emitting diodes(LEDs) with different transmitting frequency and one receiver with two PDs. Considering the receiver’s scale, the time difference of arrival of the received signals is used to determine the three-dimensional location information of the indoor receiver. In a moderate model room, the proposed algorithm is analyzed via simulation. The simulation results show that the algorithm can determine the horizontal coordinates and height information of the receiver, with the positioning error is about 11 cm, which is suitable for various indoor location-based services.