Since the deformation of embankment caused by shield construction of large-scale tunnel passing through embankment would cause anti-seepage body destruction, the Yangtze River embankment should be reinforced for seepage prevention. Taking the actual crossing river embankment of Sanchahe River section in Nanjing as an example, in which the tunnel Line N of Weisan Road crosses the Yangtze River. For the situation of scattered seepage danger in flood season, the risk elimination and anti-seepage reinforcement technology was investigated and applied. Based on field tests, a wall forming scheme and corresponding treatment technology was proposed, in which cement clay slurry was firstly poured with a solidification period of 7 to 15 days, and then the high-pressure jet grouting pile with double pipe method after the leading hole was adopted. The danger risk of the embankment was successfully eliminated. After completion of the project, the embankment has stood up to the exceeding history flood with 10.39 m water level of the Yangtze River in 2020, and the anti-seepage performance of the embankment meets the functional requirements.