The pattern of flood release is highly related with the economic development and disaster prevention in estuarine regions. Based on the measured flood data in 1998 and 2005 and the topographic data in 1999 and 2007 at the eight river mouths of the Pearl River Estuary, we investigated into the variations of flood flow allocation ratio among the mouths, and then analyzed the changes of flow allocation as well as the evolution of typical cross sections for flood release. According to the empirical equation, we further calculated the variations of the flood release ability of different river mouths. Our findings unveiled that the width of typical cross section for flood release of river mouth remained relatively stable while the depth tended to increase, beneficial for flood release. Apart from Hengmen mouth, the flood release ability was obviously enhanced due to the increased area of cross sections. The uneven downcutting of channel due to intensive sand mining is the main driving force of the changing flood flow allocation ratios, and meanwhile the significant decline of sediment supply also exert some influence.