Apple said that if confidential material got out, it would "be extremely damaging to society," a complaint claims.
This is the second time in about six months of being a Chinese citizen was accused of stealing secrets from the Apple project, whose existence the company refuses to even publicly acknowledge.
Chen first raised suspicion of Apple when his colleague announced he had taken photographs of his own-wired project with a wide-angle lens this month.
Apple launched an investigation and revealed more than 2,000 files on Chen's personal computer containing confidential information. Investigators said they also found that Chen took photos of the sensitive information displayed on the screen of his desktop, a move that went around Apple's monitoring.
The FBI said the engineer admitted that he had also backed up his Apple desktop on a personal hard drive, which is contrary to company policy.
Two photographs led in particular to an "instant criminal charge" against Chen, according to the complaint. One shows the assembly drawing of the wiring harness for the auto-wagon, and the other is a diagram showing how sensors interact with other parts of the vehicle to drive autonomously.
Chen's legal counsel, Daniel Olmos, declined to comment on the case. Chen was released last week after giving up his passport and sending $ 100,000 to bail.
According to the complaint, Apple said it would download the project information to its personal hard drive as "insurance" if it lost its work in the company. Apple later found out that it had applied for two jobs in other companies, including a Chinese autonomous automotive firm competing directly with the Apple project.
Apple's spokespersons did not immediately respond to a request for remarks outside normal business hours.
Battle about auto-drive cars
In July, Chinese engineer Xiaolang Zhang was arrested and accused of stealing business secrets while working on an Apple self-driving project. Apple investigations at Zhang began after the engineer said he was going to work for Xiaopeng Motors, a Chinese electric vehicle startup.
Zhang begged innocent.
A spokesman for Xiaopeng Motors said no apple-related information was transferred to the company and Zhang was released.
The race that brings auto-driving to the market is intense.
Rob McLean contributed to this report.