隨著宋明理學興起與理學的官學化，孔廟從祀也出現了「理學化」的現象。然而，透過考察明代相關史料，會發現奉程朱理學為官方正學的明代朝廷，並無意承襲元代的趨勢，大量進祀宋元理學家，並應積極完善孔廟中的理學道統系譜；相反地，明代新祀之宋元理學家，多非著眼其理學道統淵源，甚至從二程到朱子的完整道統系譜直至明末方全備於孔廟。此現象一來透露孔廟從祀自有其進黜的標準，同時也反映明廷有意識地在孔廟中淡化理學道統的元素，其對程朱理學的推尊僅限於做為科舉官學的層面，並非毫無上限地漫延至一切領域。

Canonization in the Confucian temple was a particularly important issue in Imperial China. As Song Neo-Confucianism increasingly became the official teachings, the process of canonization in the Confucian temple became increasingly “Neo-Confucianized.” However, a survey of the relevant historical materials reveals that the Ming court, which recognized the Neo-Confucian teachings of the Cheng brothers and Zhu Xi, in fact did not intend to follow the Yuan dynasty precedent of broadly canonizing a large number of Song dynasty Neo-Confucian scholars, and fully establishing the Neo-Confucian lineage of succession within the Confucian temple. On the contrary, it took until the end of the Ming before the complete lineage of succession from the Cheng brothers to Zhu Xi was established in the Confucian temple. These developments make clear that the canonization process in the Confucian temple followed its own standards, reflecting that the Ming court consciously downplayed the Neo-Confucian lineage of succession. The court’s regard for the Neo-Confucian teachings of the Cheng brothers and Zhu Xi was limited to the level of the civil service examinations and did not extend to other arenas.