This paper aims to elucidate the layout and structural organization of ancestral temples during the preQin period through an extensive examination of classical literature and archaeological findings. The architectural style of ancestral temples in Xia dynasty is characterized by single buildings enclosed by corridors and courtyards, while Shang dynasty exhibits a Group-type layout with multiple courtyards. In contrast, Zhou dynasty showcases a Clustertype arrangement, where several temples are juxtaposed according to the zhaomu hierarchical system. On this basis, This paper conducts an analysis and synthesis of the clustertype and isomorphic characteristics within the ancestral temple system of the pre-Qin era. This encompasses the isomorphism of architectural spaces between the temple, temple dormitory, and palace (residence), the isomorphism observed among independent temples within the Clustertype ancestral temple, and the isomorphism between the ancestral temple system and the social structure, as reflected the transition from the “scholar’s one temple” to “emperor’s seven temples”. Furthermore, it unveils the parallel information and continuous relationship between the architectural sites of pre-Qin ancestral temples and classical literary and historical sources. This study contends that the “cluster-type” and “isomorphic” characteristics of ancestral temple architecture in the pre-Qin period reflect a hierarchical ideology grounded in mathematical logic. It underscores the significance of the temple system’s philosophy, emphasizing the connection between family and the broader world through ceremonial rites.