Cottonwood Heights has a council/manager form of government, with four council members and a mayor who acts as chairman of the council. The mayor also serves as city representative in signing legal documents and attending city events.

The council and mayor select and hire a city manager as the city's chief administrative officer, responsible for enacting the council’s policies and hiring additional personnel. They must also approve appointees for city attorney, city treasurer, city recorder, and city finance officer, required by state statute.

When needed, the city council will act as the Community Development and Renewal Agency (CDRA) to undertake or promote city urban renewal, economic development and community development.