Van Zeng is accused of signing off on an inspection of his own home and inspections on two of his father's construction projects.
Zeng was charged with violating a city law that prohibits public employees from making or influencing a government decision if they have a financial conflict of interest.
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Zeng formerly worked for his father's contracting company, Mutual Seiko, before taking his position with the city, according to San Francisco District Attorney Brooke Jenkins' office.
"San Franciscans should expect our public employees to act with integrity and not engage in self-serving behavior," Jenkins said in a statement.
Zeng is due back in court on Feb. 23 for a pretrial conference.
His charges are the latest in a series of criminal cases involving the Department of Building Inspection, which has had other former employees charged in federal court as part of an investigation into corruption at City Hall.