Theodore was the fourth child of John and Phoebe (Tillotson) Miller. He married Charlotte Harris in 1849. The 1850 Federal Census shows Theodore and Charlotte living in North East Township near Erie, Pennsylvania. It's assumed that Charlotte died shortly thereafter, but no records have been found relating to her death.

In 1852, John married Lorinda Terry in Panama, NY. Lorinda's ancestry can be traced back to John and Elizabeth (Tilley) Howland, who came to America in 1620 aboard the Mayflower. Theodore and Lorinda moved to Erie, PA, where they began their family. In 1857 or early 1858, they moved westward to Olmsted County, MN.

On October 10, 1861, Theodore enlisted in Company E of the 3rd Regiment Minnesota Volunteer Infantry. In January of 1862, he went home without authorization because his family was destitute. He later enlisted with Company K of the 6th Regiment Minnesota Volunteer Infantry which was dealing with the Indian uprisings in Southern Minnesota. When it was discovered that he had deserted his former regiment, he was arrested and sent back to it. Theodore was discharged on September 2, 1865.

In 1872, yellow fever struck the family and two of Theodore's younger children died from the illness. The family later moved north to Morrison County, MN.