The channel widening rate is one of the main parameters for the stability of tidal estuaries. Based on previous methods of calculating channel widening rate via river channel width, a new method of calculating the channel widening rate of natural estuary which takes discharge section area as the main parameter is proposed in the paper. The channel widening rate from Baimao sand shoal to Wusongkou in the south branch of Yangtze estuary is calculated from 1917 to 2006. The results indicate that the overall channel widening rate has been decreasing for the past century, which adapts to the continuous scouring in the south branch channel. Meanwhile, the development of Baimao sand shoal, Biandan sand shoal, Zhongyang sand shoal, and Liuhe sand shoal has helped narrow the channel width, reduce the discharge section area and decrease the widening rate. The smallest channel width at 5m contour of Qiyakou and its function as one of the nodes in the estuary contributed to a minimum widening rate in 1979. In 2006, the widening rate increased to 1.21% owing to an increased discharge section area from Shidongkou to Wusongkou induced by deducted sediment supply after the Three Gorges Reservoir impoundment and the subsequent erosion at main sand shoals in the south branch, especially at Zhongyang sand shoal and Liuhe sand shoal. The new calculation method could truly reflect the increase of discharge capacity along the channel and the increasing rate.