The invention discloses a novel anti-backflow intercepting well control method which comprises the steps of: carrying out initial setting: monitoring a liquid level height H in the intercepting well and on the upstream of a downward opening type weir gate in real time, monitoring a natural water liquid level height H' in real time, setting a maximum anti-backflow height of the downward opening type weir gate as Hmax, setting a top height of the downward opening type weir gate in an intercepting state as H1, and setting a safety distance of a natural water liquid level and the top height of the downward opening type weir gate as a; a, when H' is greater than H and H' is greater than H1-a, controlling the top height of the downward opening type weir gate as H'+a, when the natural water liquid level is risen, ascending the downward opening type weir gate until the top height is Hmax, and when the natural water liquid level drops, descending the downward opening type weir gate until the top height is H1; b, when H' is smaller than H, controlling the intercepting well to execute a drainage procedure. The control method disclosed by the invention is simple and effective, not only can prevent backflow, but also can safely drain and draw off floodwater, regulates and controls the intercepting height of the downward opening type weir gate in real time, is sensitive in reaction, and is rapid and safe in regulating process.