In this article, a carbon cloth composite electrode modified with gold nanoparticles (AuNPs) was prepared by a facile in situ electrodeposition method and applied to the detection of mercury ions in water. With the optimized electrochemical detection conditions and methods, the limit of detection (LOD) was 0.6 μg L with the linearity ranging from 2 to 200 μg L by the SWSV detection method, and the electrode showed good repeatability after many cycles. Based on this detection method, a continuous flow electrochemical detection system was constructed and applied to the detection of Hg ions in environmental water samples. The standard addition experimental results of two real water samples with an addition level of 10 and 50 μg L showed that the recoveries were between 92.4% and 108.9% with RSDs from 2.01% to 3.22%. These results showed the same performance as that of the ZAAS mercury detection method (recovery: 94-102.4%, RSD 2.09-5.4%). Compared with other electrode materials, a shorter detection time, a wider linear range and high stability with a similar LOD can be achieved by a continuous flow detection method by using the composite electrode. The established continuous flow electrochemical detection system would have promising application in online and real-time detection of heavy metals in environmental water.