The Austrian World No.5 was too strong for Murray, who is still finding his feet as he bids to come back from hip surgery.
Thiem took the first set 6-2 and although the Scot battled back from a break down in the second set to force a tie-break, Thiem took it 7-3 to wrap up a straight-sets triumph.
Murray, who defeated Matteo Berrettini and Cameron Norrie to make the last eight in Beijing, will now move on to the Shanghai Masters next week. The 32-year-old has been handed a wildcard for that event and will discover his first-round opponent on Saturday.