Abstract: Taking flood control project between Baotou Kundulun river south bridge and Baotou-Lanzhou railway as an example，fee of flood control project investment estimate was analyzed and demonstrated from many aspects，such as compilation principle，determination of compensation standard，fee standard，analysis of compensation price of rural part，professional project construction cost，reserve funds，various taxes and fees，and other expenses etc.It provide accurate basis for rational determination of construction investment and national and local flood control project construction.