The underwater tunnel is a systematic engineering with complex conditions, large scale and high risk. Hence, the healthsafetyenvironment (HSE) risk management system is applied to Hong KongZhuhaiMacau Link (HZML) for the first time. The risk sources and risk incidents of immersed tunnel construction related to HSE are introduced; the evaluation indices of HSE risk evaluation by LEC method are determined; the HSE risk sources are identified and evaluated; countermeasures are put forward according to quantized HSE risk management object; the potential risks higher than Level 3 which would induce serious consequences should be paid more attention to and improved; and emergency plan is also made for two Level2 rick incidents of Chinese white dolphin protection and extremely abnormal weather with a significantly higher risk. The HSE risk management system has played an important role in the construction of the immersed tunnel of HZML, and good effect has been achieved.