As it produced numerous Todai-ji Betto (the head priest) in medieval times, Tonan-in Temple existed as one of the 2 major sub-temples of Todai-ji Temple with Sonsho-in Temple, which followed the teachings of the Kegon Sect that was considered as the fundamental sect of Todai-ji Temple, being the other.
中世において多くの東大寺別当を輩出したため、東大寺の根本宗ともいうべき華厳宗を継承する尊勝院とならび、東大寺の二大院家として存立していた。