It was named for Oliver Hazard Perry Throck Morton (1823-1877), governor of Indiana during the American Civil War and later a United States Senator.

After the Northern Pacific Railroad announced the location for the western approach to its Missouri River bridge, a new settlement appeared in December 1878.

Initially the US Post Office designated the riverside settlement "Morton" after the corresponding county.

[5][6][7][8] The 1,172-mile long Dakota Access Pipeline (DAPL) route submitted in its final permit applications starting in September 2014 would include a 72-mile portion through Morton County.

In August 2016 the Standing Rock Sioux Tribe (SRST) filed an injunction against United States Army Corps of Engineers (USACE) to attempt to halt construction.

In his 58-page decision by United States District Judge James E. Boasberg shows that the tribe failed to participate in the process of the USACE and Energy Transfer Partners (ETP) to address the tribes complaints.

Amnesty International wrote a letter to Sheriff Kyle Kirchmeier on September 28, 2016, requesting that he investigate the use of force by private contractors, remove blockades and discontinue the use of riot gear by Morton County sheriff's deputies when policing protests in order to facilitate the right to peaceful protests in accordance with international law and standards.

[citation needed] The Missouri River flows south-southeastward along the east boundary line of Morton County, and Cannonball River flows east-northeastward along the eastern portion of the county's south boundary line.

The county terrain consists of low rolling hills, etched by gullies and drainages; the more level areas are devoted to agriculture.