The invention relates to a method and system for automatically controlling the water level of an inverted siphon in an open channel. The system comprises an open water channel section, wherein an inverted siphon is connected with the lower reach of the open water channel section in series; a working gate is arranged at the outlet of the inverted siphon; a check gate is arranged at the upper reachof the open channel section; the check gate is provided with a water level sensor in front of the check gate, a water level sensor behind the check gate and a check gate opening sensor; a check gate opening and closing mechanism of the check gate is connected with a check gate PLC (programmable logic controller); and the water level sensor in front of the check gate, the water level sensor behindthe check gate, the check gate opening sensor and the check gate PLC are connected with a control and data processor. In the invention, as the check gate is arranged on the open channel section and is provided with the water level sensor in front of the check gate and the water level sensor behind the check gate which are matched with a water level sensor and a flow sensor which are arranged at the outlet of the inverted siphon, the optimal control data are obtained by analyzing and computing the obtained data and the water level is preciously controlled according to the data, thus ensuring safe and efficient operation.