The invention relates to a water quality detection system based on an in-situ pore water collecting water column. The water quality detection system includes the in-situ pore water collecting water column, a communication device and a water quality detection analysis device; the communication device and the water quality detection analysis device are both arranged on the in-situ pore water collecting water column, wherein the communication device is connected with the water quality detection analysis device and a control system of the in-situ pore water collecting water column; the water quality detection analysis device includes a depth sensor, a microbial sensor, a pH sensor, a temperature sensor, a heavy metal electrochemical detection sensor, a dissolved oxygen sensor, an electrical conductivity sensor, a sensor driving circuit, a data acquisition circuit and a communication circuit; the communication device includes a data coupler, data communication cables and a communication control device. While the in-situ pore water sampling column is subjected to water sample collection, the water quality of the water sample can be subjected to initial detection, so that the water sample extraction and determination work efficiency of the in-situ pore water sampling column is improved, and the using range of the in-situ pore water sampling column is extended.