Safety is essential for the great ship which are sailing in the restricted channel, by estimating the squat and the Under Keel Clearance (UKC) correctly. This paper conducted the study on the method for calculating the squat in restricted channel. While the ship is sailing in the restrictive channel, the squat is affected by ship boundary layer. In this paper, hydrodynamic theory and flat boundary layer theory were applied to put forward the approximate formula to calculate ship boundary layer. Considering the impact of ship boundary layer, the method of squat calculating was put forward. Finally, the method was verified by real ship data.