The invention discloses a multiple online control method and system. The method comprises the steps that the set temperature and the indoor environment temperature of each indoor unit are obtained, and the temperature difference is calculated; the comprehensive temperature difference is calculated; a refrigeration modification value ETS/a heating modification value CTS is calculated according to the comprehensive temperature difference; and the evaporation temperature/condensation temperature is modified, and the frequency of each compressor is adjusted. According to the multiple online control method, the frequency of each compressor is adjusted according to the modified evaporation temperature/refrigeration temperature, energy is saved, and meanwhile the refrigerating/heating effect of each indoor unit can be guaranteed. When the requirement for each indoor unit is low, the frequency of the corresponding compressor is reduced, the corresponding compressor runs at the low frequency and is kept running with the low output in a low energy consumption manner, the corresponding compressor is protected against start stop, and accordingly power rise caused by start stop of the corresponding compressor is avoided. Meanwhile, the indoor units continuously run, so that the indoor temperature is maintained near the set temperature, the constant indoor temperature is achieved, a good refrigerating/heating effect is guaranteed, and the comfort degree is improved.