Yes, it's Shirakawa Village in Gifu prefecture. I taught a seminar once in Gifu and so had a chance to visit. It is very beautiful!
While the particular shape of the roof is famous to that village, historically many buildings and houses had amazing thatched roofs. While Shirakawa gets government subsidies as a world heritage site to keep them beautiful, you can still find some authentic houses in small towns nearly as beautiful, but without the big crowds.
Unfortunately the EXTREME expense of keeping up, or replacing, those kinds of roofs have seen most old houses converting over to tin/metal or the ubiquitous tiles throughout the rest of Japan. While I can't remember exactly, IIRC it is in the hundreds of thousands to have done.