The invention relates to a crop canopy temperature and soil moisture content data monitoring system and application thereof. The crop canopy temperature and soil moisture content data monitoring system is characterized by comprising a power source management unit, a microprocessor, a multiplexing switch, a data acquisition unit, an analog-digital converter, a data storage unit, a man-machine interaction unit and a communication unit, the microprocessor and the data acquisition unit are powered by the power source management unit, the data acquisition unit transmits collected crop canopy temperature and soil moisture content analog signals to the analog-digital converter through the multiplexing switch, the analog-digital converter transmits digital signals to the microprocessor, the microprocessor transmits data with engineering units to the data storage unit and the man-machine interaction unit respectively, running configuration parameters are input to the microprocessor through the man-machine interaction unit, the running status of the microprocessor is displayed through the man-machine interaction unit, the microprocessor controls the data storage unit to transmit the stored data to a server through the communication unit and receives measuring control signals through the communication unit, and the measuring control signals are sent by the server.