The base holds the Joint Interagency Task Force South which keeps tabs on illicit trafficking in both the air and sea and is overseen by a Coast Guard Flag Officer.
Lyuyou Liao, 27, was noticed going into the military site from the rocks along the water by onlookers after travelling by foot around an outer edge fence of the Naval Air Station in Key West, according to a federal complaint.
The witnesses warned Mr Liao he was trespassing in a restricted area known as the Truman Annex, reported the Miami Herald.
US military police snatched Mr Liao’s phone and called a federal agent after they saw him taking photos with his mobile phone, the complaint said.
Mr Liao was arrested and charged with entering Naval property for the purpose of photographing defence installations.
He told a Naval Criminal Investigative Service agent that he was trying to take photographs of the sunrise, according to the complaint affidavit.
However, the agent reported finding photographs of the Truman Annex on the camera. A lawyer for Mr Liao was not listed in court records.
His arrest comes just over a year after another Chinese national was charged with taking photos at the Naval Air Station in Key West.
In September 2018, Key West police caught Zhao Qianli at the base.
The 20-year-old told federal authorities he was a music student and he lost his way on the tourist trail, but investigators found photos on Mr Qianli’s mobile phone and digital camera of government buildings and a Defense Department antenna, according to court records.
Mr Qianli was sentenced to a year in prison after pleading guilty in February to one count of photographing defence installations.
A 33-year-old Chinese woman called Yujing Zhang was arrested at Donald Trump’s Mar-a-Lago resort in Palm Beach, Florida last month.
Ms Zhang, who was convicted in September and sentenced in November to eight months in jail, was charged with trespassing in a restricted area and lying to a federal agent.
Cedric Leighton, a retired US Air Force colonel and intelligence officer, told Quartz Mr Liao’s arrest shares parallels with a continuing espionage campaign by the Chinese.
“For example, we know that China often employs ‘runway watchers or ‘aeroplane spotters’ to monitor takeoffs and landings at US airbases,” Mr Leighton said. “When I was stationed on Guam we knew that [the] Chinese were monitoring our flight activity at Andersen AFB.”
He added: “They will employ both technical and human intelligence to gain as detailed a picture of US military operations as possible.”
Additional reporting by Associated Press