The invention provides a flexible control method for the water level of a low-pressure heater under the deep peak regulating working condition of a heat supply unit. The method includes the steps thata normal dewatering control circuit controls the opening of a normal dewatering regulating valve, an accident dewatering control circuit control controls the opening of an accident dewatering regulating valve, after a normal dewatering regulating valve automatic instruction is filtered through a first inertial filtering module, the automatic instruction is sent to a first multi-point polygonal function module, a flexible factor is obtained, after subtracting the flexible factor from the constant 1, the value and a water level deviation signal of the normal dewatering control circuit are multiplied, and the value serves as an input signal of a normal dewatering control circuit controller; and the flexible factor and a water level deviation signal of the accident dewatering control circuitare multiplied, and the value serves as an input signal of an accident dewatering control circuit controller. The control manner of the water level of the heater is flexibly switched between normal dewatering regulation and accident dewatering regulation, the problem that the water level of the low-pressure heater under the deep peak regulating working condition of the heat supply unit is difficult to control is effectively solved, the operating safety and stability of the unit are improved, and losses of working media and energy are reduced.