Police said a man, identified only as Mr Xu, 41, was taken into custody and had a history of mental illness.
Air China flight CA1350 was heading to Beijing from Changsha but had to make an emergency landing in Henan province.
No passengers or crew were harmed during the incident.
Photos circulating on Chinese social media showed a man holding a cabin crew member around the neck using the pen as a weapon.
The security bureau added that the flight was forced to make an emergency landing at 09:58am local time on Sunday and was diverted to the Chinese province of Henan. All passengers were safely escorted off the aircraft by 10:50am.
Mr Xu, who is said to be from Hunan’s An Hua county, was later taken into custody with police now looking into the incident. The security bureau did not add when, or if, he had been released.