Hill tweeted in response to Mississippi Gov. Tate Reeves, who posted on Twitter that a proposal among some in the state legislature to create a second Mississippi flag "does not meet the threshold" and would "divide our state more."
In response, Hill tweeted, "Either change the flag or I won't be representing this State anymore & I meant that .. I'm tired."
In a subsequent tweet, Hill, who was born and raised in Mississippi, cited the flag's controversial history for his ultimatum.
Last week, the NCAA expanded its Confederate flag policy to prohibit all its championship events from being played in states that fly the flag, including regional sites in sports such as baseball, softball, lacrosse and women's basketball.
Mississippi is the only state flag that features the banner of the Confederacy -- a blue cross with 13 white stars.
SEC commissioner Greg Sankey also threatened to not hold future championship events in the state, saying "it is past time for change to be made to the flag of the State of Mississippi."
On Monday, the Conference USA board of directors voted not to hold conference championship events in Mississippi until the Confederate emblem is removed from the flag.
Several state universities, including Mississippi State and Ole Miss, stopped flying the flag in 2016.
Hill, one of the top returning backs in the SEC, rushed for 1,350 yards and 10 touchdowns last season and has 2,477 yards rushing in his career.