The design lowest navigable stage of Jialing river downstream waterway affected by unsteady flow of hydropower station is researched. Based on the analysis of the downstream water stage of hydropower station, storage outflow in the period of 2009—2010 and hydropower station operation mode in the Jialing river, we calculate the design lowest navigable discharge of downstream waterway of hydropower station using storage outflow in different time scales, and calculate the design lowest navigable stage of downstream waterway of hydropower station by water stage linear correlation between water gauges.