A handshake synchronization method and system based on visible light communication are provided. The method includes: connecting, by a transmitting end, in which a state machine varies with unit time, to a receiving end, the status of a state machine of the receiving end being synchronized with the status of the state machine of the transmitting end; using, by the transmitting end, a pseudocode signal which varies with unit time, to scramble an original signal and a pilot optical signal, and sending, in the form of a visible light signal, the scrambled signal obtained by scrambling; and receiving, by the receiving end, the visible light signal, identifying the scrambled signal of the current period of time by using a pilot optical signal, and decrypting the original signal according to the scrambled signal. Since a visible light signal which is transmitted between a transmitting end and a receiving end is not an original signal, the security of a photonic Internet of Things is improved.