A controlling method of an indoor air environment quality cooperation and control system includes: sensing whether there is an indoor person; if not, turning off an air conditioner system and a purification system, judging the values monitored by an outdoor pollutant sensor and an indoor pollutant sensor, if the value monitored by the outdoor pollutant sensor is greater than that monitored by the indoor pollutant sensor, turning off a fresh air system, otherwise starting the fresh air system; if an indoor person is sensed, calculating an IAQI according to values transmitted by a temperature and humidity sensor and the indoor pollutant sensor; calculating a ratio R of a ΔIAQI and an energy consumption increase value ΔP, and selecting a regulation mode with the maximum ratio R to coordinate a quality of the indoor environment; and returning and executing the sensing step.