A defogging control system includes a plurality of first heating wires, a plurality of second heating wires, an electrical sensor and driver, a timer, an environment sensing module, and a control module. The electrical sensor and driver is utilized to generate a start signal or a stop signal, corresponding to a controller of a refrigeration storage apparatus. The timer is utilized to count a real-time operation time and record a previous operation time. The environment sensing module is utilized to sense a temperature and a humidity. The control module is utilized to control the first heating wires and the second heating wires by the real-time operation time, the previous operation time, the temperature, and the humidity. Further, a defogging control method is also provided.