The present invention discloses a karst fissure water detection system and method. According to the karst fissure water detection system and method, a pumping and injection well is drilled at the center of a region to be detected, geological boreholes are drilled with the pumping and injection well as a center; water is pumped from the pumping and injection well, water pumping time, pumped water quantity as well as the water level changes of the pumping and injection well and the geological boreholes are recorded; salinity sensors and water temperature sensors are distributed, and the salinity sensors and the water temperature sensors are connected into a computer through a data acquisition module so as to acquire the initial salinity and water temperature of karst fissure water; the salinity change of the karst fissure water in each borehole is acquired in real time until values acquired by some salinity sensors obviously changes, and hot water is injected into the pumping and injection well, and the temperature change of the karst fissure water in each borehole is acquired in real time until values acquired by some water temperature sensors obviously changes; and the permeability, flow direction, flow rate and main water channels of the karst fissure water are analyzed.