Hekou Yao Autonomous County belongs to Jinsang County, Zhang Si County. The Ming Dynasty was the court of the king of Lin 'an prefecture. In the 23rd year of Guangxu reign in Qing Dynasty (1897), the Estuary Flood Control Office was established. In the 15th year of the Republic of China (1926), Hekou was designated as a special administrative region.

Hekou City was founded in 1950. The red and white rivers will meet here, hence the name. 1955 changed Hekou County, 1963 changed Hekou Yao Autonomous County.

In 2000, Hekou Yao Autonomous County administered 2 towns and 4 townships: Hekou Town, Nanxi Town, Yaoshan Township, Lianhuatan Township, Laofanzhai Township and Qiaotou Miao and Zhuang Township.