Apple said that if the confidential material came out, it would be "enormously damaging" for the company, the allegations are filed.
The second time for about six months is a Chinese citizen is accused of stealing secret from the Apple project, whose existence the company refuses even publicly admitted.
Chen first raised suspicion in Apple when a colleague reported that he photographed him earlier this month with a auto-engine with a wide-angle lens.
Apple has launched an investigation, revealing more than 2,000 files on Chen's personal computer that contain confidential information, according to court documents. Investigators also said Chen recorded sensitive information on his computer, which was bypassing Apple's network monitoring.
The FBI said the engineer admitted he had also supported his Apple computer for personal property, which is contrary to the company's policy.
Two photos specifically led to "instant criminal charges" against Chen, according to complaints. One shows a group drawing of wicket bundles for the car that drives itself, and another diagram that shows how the sensors communicate with other parts of the car to drive autonomously.
Chen's attorney, Daniel Olmos, refused to comment on the case. Chen was released last week after handing over his passport and publishing $ 100,000 with the bail.
He complained to Apple that the project data had been transferred to his personal hard drive as a "security pole" if he lost his job at the company. Apple later learned that she applied for two jobs in other companies, including a Chinese company that directly deals with Apple's project.
Apple spokespersons did not respond promptly to a comment outside regular business hours.
The battle about car driving
In July, Chinese engineer Xiaolang Zhang was arrested and charged with stealing business secrets while working on the self-service project of Apple. Apple's Zhangu investigation began after the engineer said he was leaving for Xiaopeng Motors, the Chinese launch of electric vehicles.
Zhang pleaded not guilty.
Xiaopeng Motors spokeswoman said Apple did not share Apple's information and that Zhang was released.
The race to drive the car to the market is intense.
Rob McLean contributed to this report.