The blaze at the Maison des Bois, at Manigod, 1,800 metres high up in the Alps of the Haute-Savoie, began at around 2am on Tuesday.
According to reports the fire started in the linen room and then spread to the roof leaving most of the restaurant destroyed.
Around 60 firefighters were called out to fight the blaze, with one of them ending up in hospital needing treatment for smoke inhalation.
Firefighters had extinguished the blaze inside the restaurant by mid-morning but were still battling to bring the fire under total control as it ravaged the roof of the wooden structure.
The owner Marc Veyrat, considered by some to be the best chef in France, was at the scene along with the mayor of the town.
"This is a life and a piece of French cultural history that has just goneup in flames," Veyrat told AFP.
"It's not just a restaurant but also a museum of popular art showing several pieces of furniture from the region. It's sad, but I'm a fighter. I'll be back," said Veyrat.
The highly acclaimed Veyrat is little known outside France but he is one of the stars of the French gastronomy scene and obtained a total of six Michelin stars in the past – (three stars for each of his other two restaurants).
He was also the first French chef to get the perfect grade of 20/20 in the respected Gault-Millau guide.
(Marc Veyrat in his Maison des Bois restaurant. Photo: AFP)
The Maison des Bois was his pride and joy and took two and half years to design and build before it finally opened in 2013.
Veyrat specialises in traditional dishes, with lots of wild herbs and a little "molecular gastronomy", chemistry-inspired recipes that produce new textures such as emulsions in cuisine.
Veyrat was badly injured in a skiing accident in 2006 after colliding with his daughter on the slopes near Megeve.
He handed back the six Michelin stars he had won (for two separate three-star restaurants) and only in 2013 re-entered the kitchen, opening his Alpine restaurant.
But such Michelin-starred genius does not come cheap.
According to his website, the top 12-course tasting menu at La Maison du Bois would set the diner back €325 ($344).