Knowledge of population size and migration ecology is essential for the conservation of endangered migrants. We studied the wintering population size and migration of Black Stork (Ciconia nigra) at the Napahai Wetland in Yunnan province during October-April 2004-2005, 2007-2008 and 2008-2009 by roosting sites counting. Our results showed that the Napahai Wetland was one of the most important wintering and stop-over sites of Black Stork in China. The average population size was 39.6, 128.6 and 181.8 in winters of 2004-2005, 2007-2008 and 2008-2009, respectively. The Napahai Wetland was also an important stop-over site for Black Stork populations migrated from Mongolia to India. The Black Storks normally migrated to Napahai in late October and left in mid-or late March. We suggested local government take effective measures to manage the wetland and protect Black Storks, including maintaining enough shallow water areas as their feeding sites and decreasing human disturbances.