Despite being destroyed twice (in 1574 and 1615) and bombed in 1945, three original Edo-period structures survived: the Main Hall (1654), the two-story Sanmon gate (1647), and the ornate Karamon gate.

The Buddha Hall features a ceiling painting of a dragon that appears to glare at you from every direction you view it, a rare artistic technique called 'happo nirami-no-ryu' (dragon glaring in eight directions).

Il giardino secco di Nanshu-ji fu realizzato da Furuta Oribe nel 1619 ed è designato Luogo Nazionale di Bellezza Paesaggistica.

The temple houses a monument claiming to be the true grave of Tokugawa Ieyasu, based on a legend that he was killed during the 1615 Siege of Osaka and secretly buried here, contradicting official history.