The temple holds various historically significant structures. Soshi-do (Founder’s Hall), designated a national cultural treasure, was rebuilt in the Enpo era (1673-81). Other national cultural treasures are the Hokke-do main hall, built in the Muromachi era, and the Shisoku-mon gate. Hokke-do is the oldest structure and believed to be the main structure of Honmyoji. Goju-no-to (the five story pagoda), built in 1622, is also the national treasure. There is a substantial addition, Shogyo-den, built in 1931. Others include are: Kishimojin-do, Aragyo-do, and Joshuden (the guest house.)

The temple maintains numerous sacred national treasures as well: Nichiren Shonin’s original “Rissho Ankoku Ron,” “Kanjin Honzon Sho,” and 56 volumes of his original writings. These are shown to public only once a year on November 3. Countless numbers of historical documents, the statue of Nichiren Shonin, various other statues, and sacred artwork all dating back to the Middle Ages.