The invention belongs to the technical field of air conditioners, and discloses a three-pipe system multifunctional multi-connected air conditioner system and a control method thereof. The system comprises a compressor, a condenser, a machine room evaporator and indoor evaporators. The first end of the condenser communicates with an inlet and an outlet of the compressor through two branches. The first end of the machine room evaporator communicates with the inlet of the compressor, and a second throttling device is arranged at the first end of the machine room evaporator. First throttling devices are arranged at the second ends of the indoor evaporators and the second end of the machine room evaporator. The second ends of the indoor evaporators, the second end of the machine room evaporator and the second end of the condenser communicate with one another. According to the three-pipe system multifunctional multi-connected air conditioner system and the control method thereof, a many-online machine and a machine room air conditioner are coupled with each other and can independently work, the problems about small-load running, lubricating, oil returning, frosting and defrosting, starting and stopping and the like of the many-online machine can be solved, waste heat of a machine room is recycled, space is saved, and equipment cost is reduced; and due to the second throttling devices, the machine room evaporator and the indoor evaporators have different evaporation temperatures, and the refrigerating effect of the machine room evaporator is guaranteed.