The invention relates to an in-situ detection system for concentration of deep sea micro-ions. The in-situ detection system comprises two sub-systems including a liquid path system and a control system. According to the system, a flow injection analysis technology is taken as an automatic continuous flow analysis method to realize feeding, mixed reaction and automation of detection, and the system has four working modes including calibration, detection, flushing and standby, the self-maintenance flushing and calibration are realized, and the system can be resided in the deep sea environment to carry out the in-situ detection. A liquid core waveguide with the length of 5 meters is taken as a detection pool of the system, so that the pre-concentration or pre-enrichment process in the conventional detection method is reduced, the system is simplified, the detection efficiency is improved, the sample consumption is decreased, the sensitivity of the system is effectively increased, and the detection limit is lowered, and the system is suitable for detecting the trace elements in the deep sea.