The invention discloses a method and a system of clock distributing in an ocean seismic survey system, the method and the system are applied to a multiple marine seismic streamer system and the method includes: a master control work station sending command data embedded into clocks to cascaded marine seismic streamer interface boards in levels of marine seismic streamers through a high speed serial channel in sequence; after receiving the command data embedded into the clock, the marine seismic streamer interface boards in levels of marine seismic streamers extracting the embedded clocks, and sending the clocks to all the digital packets in the marine seismic streamer at the same level in sequence through a downward command channel; and after receiving the clocks in the downward command channel, tail packets in levels of marine seismic streamers enabling the clocks to pass through all the digital packets in the marine seismic streamer at the same level in sequence and looping the clocks back to the marine seismic streamer interface board at the same level. The clocks of all the modules can be enabled to be accordant in frequency, and synchronism of the ocean seismic survey system is ensured.