The state did not adopt the flag—which featured three red, white and blue bars with a Confederate cross in the upper left-hand corner—until 1894, almost three decades after the end of the Civil War and several years after the end of Reconstruction. White supremacist lawmakers adopted the Confederate-themed flag in place of a prior magnolia flag as they worked to lock Black Mississippians out of politics with a slew of Jim Crow laws.
https://www.mississippifreepress.org/34094/senator-calls-for-return-of-old-mississippi-flag-our-people-died-under-that-flag