The invention provides a fresh air conditioner control system and a control method thereof. An air conditioner comprises an indoor unit body and a fresh air device, the fresh air device is arranged outside or inside the indoor unit body in a linkage manner, and is used for providing outdoor fresh air to the room, the control system comprises an environment detection device, a cloud server and a controller, and is arranged in the indoor environment, the environment detection device comprises an air quality detector, a temperature detector and a data transmission interface, and the controller obtains the air quality difference value and the indoor temperature difference value which are calculated by the cloud server, if the air quality difference value is larger than zero, the controller controls the fresh air device to run, if the air quality difference value is smaller than or equal to the zero, the controller controls the fresh air device to be turned off, if the indoor temperature difference value is larger than zero, the controller controls the air conditioner to run in a refrigeration manner, if the indoor temperature difference value is smaller than zero, the controller controls the air conditioner to carry out heating running, and if the indoor temperature difference value is equal to zero, the air conditioner does not run.