In this paper, automatic control of the water level in an irrigation canal by automatic regulation of intermediate gates was studied. Previous scholars have proposed a water level difference control strategy that works to keep relative deviations in all pools the same for a particular situation where the operator does not have full control over the canal inflow, with the centralized linear quadratic regulator (LQR) control method used. While in practice, the deviation tolerance of pools may differ in some canals which limits the applicability of the control strategy. In this work, a weight coefficient was added to the deviation and the algorithm was improved to keep the relative deviations to certain proportions. The model predictive control (MPC) method was then used with this improved control strategy and was compared to the LQR control method using the same control strategy. The results showed that the improved strategy can keep the water level deviations in all pools to certain proportions, as is our objective. Also, under this difference control strategy, the MPC method greatly improved the control performance compared to the LQR control method.