The invention discloses a control method, system and device of a water chiller-heater unit and an air conditioner. The method comprises the steps that the operating mode of the water chiller-heater unit is judged; under the condition that the operating mode of the water chiller-heater unit is a non-refrigerating mode, the water outlet temperature of a pipe shell of the water chiller-heater unit is detected; and under the condition that the water outlet temperature of the pipe shell is smaller than or equal to first preset water outlet temperature, the operating mode of the water chiller-heater unit is controlled according to the temperature difference change rate and the water outlet temperature, wherein the temperature difference is the difference between the water outlet temperature of the pipe shell and the water inlet temperature of the pipe shell. According to the control method, system and device of the water chiller-heater unit and the air conditioner, the technical problem that in the prior art, due to the fact that the volume of a flooded pipe shell of a water chiller-heater unit is small, cracking is prone to happening after water in the pipe shell becomes icy fast is solved.