Abstract: Aiming at the shortage of a common experiential shoal-biased method assuring navigation safe, a method for controlling shoal-bias based on uncertainty is proposed. Uncertainties of raw depth and interpolated depths are calculated, a safe and reliable model for controlling shoal-bias with a quantitative value based a depth uncertainty is designed, and the probability of two depth models assuring navigation safe are compared and analyzed. Experimental results demonstrate: The proposed method is much more reliable in security than that of the experiential shoal-biased binning method, especially in areas where depths change complexly.