It happened at the store on 100 Greaves Ln. around 3:45 p.m.
Officials say the store was open for business and busy with customers preparing for the holiday.
According to the FDNY, surveillance video shows 21-year-old Dominick Sacchetti starting the fire on a shelf stocked with paper goods.
The flames spread quickly, causing an estimated $100,000 in damages.
A quick-thinking shopper used a fire extinguisher to control the flames before firefighters arrived.
No injuries were reported.
Sacchetti is charged with multiple accounts of arson, two counts of reckless endangerment, and two counts of criminal mischief.
"While residents of Staten Island were beginning to prepare for Thanksgiving with their families, this individual put the lives of shoppers and responding firefighters at risk," said FDNY Commissioner Robert S. Tucker.
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