Echo24.cz portal published an article on top 10 Czech Restaurants for the year 2016; the ranking is based on Maurer's Selection Grand Restaurant. The nation-wide survey focused on cuisine, service, interior design and price, for example.  

The Top 10:

1. Radisson Blu Alcron Hotel, Alcron (Prague)
2. Terasa U Zlaté studně (Prague)
3. Bellevue (Prague)
4. Chateau Mcely, Piano Nobile (Mcely)
5. Aria Hotel, CODA Restaurant (Prague)
6. Pavillon (Brno)
7. Promenáda (Karlovy Vary)
8. La Degustation Bohême Bourgeoise (Prague)
9. InterContinental hotel, Zlatá Praha (Prague)
10. Nautilus hotel, Goldie (Tábor)

The Top 100 ranking and more details in Czech are available here.