The embodiment of the invention provides an intelligent modular control system and a control method thereof. The intelligent modular control system comprises a control module, at least one compressor, at least one fan and at least one condenser, wherein the compressor, the fan and the condenser are connected through pipelines; the control module comprises a main control module, a fan control module and a compressor control module, wherein the fan control module and the compressor control module are respectively connected with the main control module; the fan control module is used for controlling start and shutdown of each fan according to the state of the environment where the fan is; the main control module is used for controlling start and shutdown of the condenser and determining start and shutdown of the compressor according to received data information.