Volatile halogenated hydrocarbons (VHCs) attracted many attentions due to its toxic and persistent in the environment. In this research, a novel in situ ecological restoration reactor was applied to the degradation of VHCs in polluted river water. The optimized working condition adaptation of the in-situ restoration technique was evaluated through orthogonal tests. The experiments showed that when the water depth was 0.4 m, the HRT was 5d and the current velocity was 1 m/s, VHCs removal efficiencies could achieve favorable value. The CHCl3 CCl4, C2HCl3 and C2Cl4 removal efficiency could reach 70.27%, 70.59%67.74% and 81.82%, respectively. F test results showed that both HRT and water depth were significantly related to the removal efficiency of reactor. Besides, using underwater modulated chlorophyll fluorometer analyzed the rapid light curves (RLC) of plants in the experiment, which showed that the VHCs of damaged river was harmful to the physiological state of the plants. Moreover, the microbial community structures of fillers in the reactor were tested by high-throughput sequencing, the findings supported that the microbial community made a great response to adapt to the changes of environment of the reactor. The relative abundance of Rhodocyclaceae increased slightly, which hinted that it had good adaptability to VHCs in polluted river water. The research results confirmed that in situ ecological restoration reactor was an economical technology for removal VHCs in polluted river water.