The discharge at Datong station may be not entirely representative of net discharge into the East China Sea due to water abstraction and precipitation along the lower Yangtze River. Therefore, Xuliujing station, which is much nearer to the river mouth, is chosen to accurately estimate the net discharge in this paper. The Multi-Profile Method that considers the cross-sectional variability of flow is applied at Xuliujing station to estimate the tidal discharge. Then, the low-pass filter is used to remove the effects of the tide and the net discharge is obtained. Lastly, the net discharge in Datong and that in Xuliujing are compared. The results show that the net discharge of Xuliujing is obviously larger than that of Datong in the rainy season due to precipitation, but the net discharge of Xuliujing is slightly smaller than that of Datong in the dry season due to persistent abstraction and less precipitation. Therefore, in some degree, the net discharge of Xuliujing is more representative than that of Datong regarding the discharge into the East China Sea.