Cottonwood County is a county located in the U.S. state of Minnesota. As of 2000, the population was 12,167. Its county seat is Windom.

Cottonwood County was established July, 29, 1870. It was named after the Cottonwood River which runs through the northeast corner of Germantown Township. The river received its name from the abundance of cottonwood trees on its banks.

Minnesota Governor Austin appointed three county commissioners when the county was established. They met at a private home about six miles northwest of Windom on the Des Moines River at Big Bend. During this meeting, they designated the commissioners districts and changed various county officers. In the fall of 1870, the first general election was held. The first deed on record was filed on January 10, 1870. The first land assessments were made in 1871, and in 1872, the first taxes were paid.