The invention discloses a control system of an organic waste gas catalytic burner and an operation method of the control system. The control system comprises a central controller, a configuration storage, a collection module, a control module and an execution mechanism; the configuration storage, the collection module, the control module and the execution mechanism are all connected to the central controller; the collection module comprises a temperature collection module, a concentration collection module, a valve collection module and a wind amount collection module, the control module comprises a heating module, a valve module, a wind amount module and an alarm module; the execution mechanism comprises a catalysis chamber, a reversing valve, a draught fan, an air inlet valve, an emergency valve and an alarm device; a control system and a waste gas inlet and outlet mode of a traditional organic waste gas catalytic burner are changed, through the circular air inlet and outlet manner of multiple burners, the influence of heat generated by waste gas in the combustion process on a catalyst in the burner can be thoroughly avoided, the generated energy is led into a heat storage chamber of the burner to be preheated through a pipeline in a gas inlet and outlet manner, and the energy utilization rate is high.