The invention relates to a low-temperature storage control method for purging and dewatering of a fuel cell engine. The low-temperature storage control method comprises the following steps of: 1) controlling load current, controlling a heater and a radiator to maintain the temperature of inlet cooling water of a fuel cell stack, controlling a rotating speed of an air compressor, and detecting thevoltage of each single cell of the fuel cell stack through a single voltage inspection unit; 2) controlling the load current by means of a fuel cell controller, controlling a heater and a radiator tomaintain the inlet cooling water temperature of the fuel cell stack, enabling air at an outlet of an air compressor to directly flow into an air inlet of the fuel cell stack without passing through anintercooler and a humidifier, controlling an inlet and outlet switching path of a first three-way valve in a hydrogen loop to enable hydrogen at an outlet of the proportional valve to directly flow into a hydrogen inlet of the fuel cell stack after passing through the dryer, and controlling the opening degree of the proportional valve to make air pressure at an inlet of the fuel cell stack to be0-20 kPa. The low-temperature storage control method does not depend on an internal resistance online test and humidity soft measurement instrument and method, and can accurately control the water content of the fuel cell engine stack.