The three, said to run a cyber security firm in China, targeted Moody's Analytics, Siemens and Global Positioning System maker Trimble, the indictment says.
The three defendants were identified as Wu Yingzhuo, Dong Hao and Xia Lei.
It said the three sent "spearphishing" emails to computers in western Pennsylvania and around the world.
Boyusec's links to Chinese intelligence were disclosed by the Washington Free Beacon in November 2016. The operation in question allegedly started in 2011, when the hackers gained access to the unidentified economist's account and began forwarding all of their emails to an account controlled by themselves.
The hackers were charged with conspiracy to commit computer fraud and abuse, conspiracy to commit trade secrets theft, wire fraud, and aggravated identity theft. About 275 megabytes of computer files were stolen from Trimble, many with confidential or proprietary information and trade secretes about a new project by the company.
The indictment, largely symbolic, is the second major case against Chinese hackers.
The three workers were said to be in charge of a cyber security firm in China.
A Chinese internet security firm that researchers say is behind sophisticated attacks on Western energy and defense companies disbanded this month amid USA accusations that some of its shareholders were involved in hacking and theft of trade secrets.
Those hackers, part of a Shanghai-based hacking group known as Unit 61398, are believed to be in China.
"The Justice Department is committed to pursuing the arrest and prosecution of these hackers, no matter how long it takes, and we have a long memory", said Dana Boente, acting assistant attorney general for national security, on Monday.
The three alleged hackers live in China, and it's unclear if they'll ever appear in US court. They probably managed to gain access to "hundreds of gigabytes of data regarding the housing finance, energy, technology, transportation, construction, land survey, and agricultural sectors".
The indictment says that Wu (aka "mxmtmw", "Christ Wu", "wyz") and Dong (aka "Bu Yi", "Dong Shi Ye", "Tianyu") are founders and equity shareholders of Boysec, while Xie (aka "Sui Feng Yan Mie") is an employee.
Xi, a Boyusec employee, also lives in Guangzhou.
The investigation that led to the charges being filed was conducted by the FBI, the Naval Criminal Investigative Service and the Air Force's Office of Special Investigations. "A low key reaction could mean these people were freelancing".
Security researchers say attacks attributed to Boyusec have been seen at least through September.
A Chinese government spokesman didn't immediately respond to a request for comment.
Cyber-attacks have been a sensitive issue between the US and China for a number of years.