The incident happened around 6 p.m. at the JD Hoyu Grocery store at 9th and Porter Streets.
Police said Xiaoding Li, the 31-year-old son of the store's owner was found lying behind the counter by a customer.
Paramedics arrived to find the man had been shot once in the chest. He was taken to Jefferson Hospital where he later died.
A neighbor who shops at the store a lot says he saw the police activity and ran to find the family, who he says work at another nearby store.
"I just pray for the best for the father, the mother, the son and the child that he left behind also," said Jason Ortiz of South Philadelphia. "The kid didn't deserve it and there's no money in the world that's worth a life."
It's unclear if anyone else was inside the store as shots rang out.
Police are still investigating a motive for the shooting.
"It's unknown at this time if it was a robbery, we're not certain. The cash register was still in the cashier booth. We don't know if anything was taken from the cashier booth," said Chief Inspector Scott Small with the Philadelphia Police Department.
No arrests have been made.
Anyone with any information is asked to call police at 215-686-TIPS.