Jefferson City is the capital of the U.S. state of Missouri. As of the 2010 census, its population was 43,079, making it the 15th largest city in the state.It is also the county seat of Cole County, although a small portion of the city extends into Callaway County.efferson City is home to Lincoln University, a historically black college founded in 1866 and later designated as a land-grant university. In 2013, Jefferson City was named America's Most Beautiful Small Town by Rand McNally.