Phu Quoc scored 95.51 points, an increase of 0.15 points from last year, according to the magazine's annual Readers' Choice Awards.
Malaysia's Langkawi ranked second, followed by Thailand's Koh Samui.
Bali Island, which held the top spot last year, was pushed to the sixth position this year, after Boracay and Palawan of the Philippines.
Phu Quoc has become a bright spot of Vietnam's tourism this year.
The island received 1.2 million foreign arrivals between January and September, up 65.8% year-on-year and surpassing this year's target of 1 million.
So far this year, Phu Quoc has welcomed 6.5 million visitors including domestic travelers, already surpassing last year's total of 5.9 million, according to An Giang Province's Department of Tourism.
More than 757,000 Condé Nast Traveler readers participated in the survey, sharing their opinions on various travel experiences, including cities, islands, hotels, resorts, cruise ships, spas, and airlines.
The Readers' Choice Awards, the longest-running accolade in the travel industry, celebrate excellence in hotels, resorts, and destinations around the world.