The invention discloses an underground water resource online monitoring system and a detection method thereof. A main control system, a data receiving device and online monitors are arranged in an underground water resource monitoring zone, wherein a plurality of online monitors, at least three online monitors, are arranged in the underground water resource monitoring zone; the data receiving device receives data information sent by the online monitors, and transmits the data information to the main control system; the main control system processes the received data information, and sends instructions to the online monitors for real-time monitoring; each online monitor is composed of a rainwater receiver, a metering skip bucket, a control recorder, a conveying device support frame, a conveying device, a measurer, a protective cover, a rainwater metering device, a data sending device and an underground water observation well; and an online monitor is arranged on each underground water observation well. The underground water resource online monitoring system is scientific in design, reasonable and compact in structure, simple and convenient in operation, detachable, simple and convenient in disassembly and assembly and convenient to carry, can be used for monitoring the water level and the water quality of underground water after raining, is efficient and real-time, and can reduce monitoring errors.