A raft culture system capable of controlling a water layer consists of a boom rope, a balance floating ball string, an anchor rope, a fixed floating ball, a water layer regulation floating ball, a depth regulation rope, a balancing weight, a stake anchor and the like. The boom rope is provided with the balance floating ball string and the depth regulation rope; the water layer regulation floating ball is tied to the upper end of the depth regulation rope, and the balancing weight is tied to the lower end of the depth regulation rope; the culture water layer is controlled by controlling the length of the depth regulation rope; submergence of the boom rope is favorable for improving wind and wave resistance of the raft system in stormy weather and adapted to requirements of different cultured objects for the culture water layer. The system has simple machining process, convenient operation, long service life, is favorable for wide popularization and is adapted to the requirements for moving the raft facility culture offshore.