The invention relates to a data transmission method and system based on intelligent substation clock synchronization. The method includes the following steps: analyzing a message type corresponding toa data stream according to a transmission mode of the data stream; and assigning an output priority to the data stream according to the message type, and mapping the data stream to an output queue ofa corresponding switch for transmission. According to the data transmission method and system based on intelligent substation clock synchronization provided by the invention, through the steps of analyzing the message type corresponding to the data stream according to the transmission mode of the data stream, assigning the output priority to the data stream according to the message type, and mapping the data stream to the output queue of the corresponding switch for transmission, PDEelay_Rep and PDEelay_Resp messages can be preferentially forwarded even if the messages are in a network congestion state, the bidirectional path delay is basically the same, and the final time synchronization accuracy can be greatly improved.