In order to automatically and safely control long distance water delivery projects in winter, there is a need for a reasonable and feasible transition mode to avoid the emergence of ice jam. Based on open canal hydraulics, a mathematical model of canal system operated by constant downstream depth method is developed. The principle of combining feed-forward control of discharges with feedback control of water level is adopted for operation of check gates and a simulation model of multiple serial canal sections is established. Also, reasonable parameters of proportional-integral (PI) controller and logical dead band are obtained by trial and optimizing. The model is applied to simulate the operation process of the canal sections part of the main canal of the middle route of the South-to-North Water Transfer Project in China. Flow velocities are reduced to less than 0.4 m/s by decreasing discharges of canal pools and turnouts in terms of 3 days' cold current forecast in advance. As a result, discharge in canal was reduced from 70% designed capacity to less than 30%, which is a big challenge for the controller. This paper tests the suggested transition mode from open-channel water transfer state to a low flow ice-forming state at the MATLAB platform, and the results show that this model can achieve the expected goals.