After the tunnel-shield-driving machine excavated through the north levee of Yangtze River, several transverse cracks appeared in the river embankment, and the accumulative settlement of the embankment was massive. This paper investigates the influence of cracks in the embankment construction of different depths on the seepage stability of the Yangtze River embankment. Based on the three-dimensional saturated - unsaturated seepage finite element method, the three-dimensional finite element seepage analysis model of the embankment in the tunnel crossing section was established. The seepage behavior of the embankment under different crack depths within the highest water level in history is calculated. The results show that the deep mixing pile reduces the water head obviously. The through cracks have great influence on the seepage field of the stratum around the cracks. When the crack depth is less than 8.5 m, the maximum seepage gradient of dam foundation and dam body is 0.181 and 0.206 respectively, which is less than the allowable seepage gradient of corresponding soil layer, indicating the seepage stability of the embankment can meet the requirements.