The loss drops TSU's overall record to 12-10 and 6-3 in conference play. The Tigers have also lost their last three contests.
Miller finished the game with a team-high 19 points on 5-of-10 shooting and a 9-for-10 line from the charity stripe.
TSU shot 50 percent from the field (22-of-44) but just couldn't overcome Morehead State's 87.5 mark from the free throw line (28-of-32).
Tennessee State won the tip and started the game on a 6-0 run thanks to buckets by Miller, Thornton and Cyphers within the opening minute-and-a-half.
The trio accounted for 85 percent of the team's first half points (35-of-41).
TSU eventually raised its lead to 11-4 when Miller canned a pair of free throws. Miller's trip to the line was caused by MSU's seventh team foul that occurred with over 16 minutes left in the first period.
TSU made 11 of its 15 free throw attempts during the first 20 minutes for a 73.3 percent conversion rate.
Morehead State (11-11, 5-3 OVC) only fouled the Tigers three more times the remainder of the half, allowing the Eagles to get back into the game.
After Miller's makes at the charity stripe, MSU used a 19-10 swing to take a two-point lead with nine minutes left in the opening stanza. The sudden change in fortune caused TSU head coach Travis Williams to use his first timeout.
From there, the sides swapped the lead six times, but Miller was finally able to break the spell with a jumper from inside the lane with only four seconds remaining until halftime. Miller buried the shot, letting TSU carry a 41-39 advantage heading into the locker room.
The Eagles started the second half strong, and quickly made the score 47-41 in their favor. Two turnovers and two Tiger fouls allowed the MSU hot start.
Thornton finally ended the Morehead State streak with a layup at the 17 minute mark and M.J. Rhett threw down a dunk on TSU's next possession. The flushes from the TSU forwards were part of a 10-2 Tiger run that gave them a 51-49 lead.
Rhett finsihed with seven boards, leading the team for the seventh time this season.
The game remained tight from that point with five ties and four lead changes. However, MSU never trailed once Bakari Turner nailed a three at the 4:18 mark.
During the game's last four minutes TSU had three turnovers, eight fouls and zero made field goals (0-of-5). TSU's play down the stretch allowed the Eagles to finish the game on a 19-9 run.
TSU lost the battle of the boards, 29-25, and had six more turnovers (17) than the Eagles (11). Those numbers led to 41 MSU points on second chance hoops and points off of turnovers.
TSU will return home on Jan. 31 to take on Tennessee Tech. Tip-off is scheduled for 7 p.m. and the matchup will be broadcast on the OVC Digital Network.