Erdene Zuu is the oldest extant Buddhist temple in the country of Mongolia, founded following the reintroduction of Tibetan Buddhism to Inner Mongolia in the sixteenth century. The subject of this paper is the building activities of the sixteenth and seventeenth centuries, particularly of the complex centering on Gurban Zuu (Three Temples), which are the main buildings of Erdene Zuu. The author first confirms Gurban Zuu’s ground plan based on measurements, and then interprets the “black-ink inscription” discovered on the ridge purlin of the Central Buddha Hall. This complex is then compared with Inner Mongolian Buddhist temples of the same period. Finally, the author studies whether or not the spatial structure of the temple architecture of the Mongolian Empire of the thirteenth and fourteenth centuries was continued at Erdene Zuu, and analyzes the position that Erdene Zuu occupied in the Tibetan Buddhist sphere. This comparative study investigates the origins of Erdene Zuu’s architectural spatial composition within East Asia.