Any effort to understand the transformation of knowledge in modern China must take into account the changes in traditional scholarship over the past four centuries. There is thus a need for a new examination of Qing scholarship, and this article suggests a new perspective on the transformation of Ming-Qing scholarship and the reintegration of traditional learning—especially in regard to the core of Qing scholarship, the evidential studies movement of the Qianlong and Jiaqing reign periods. This new perspective might be tentatively summed up as “the critique of the ‘orthodox transmission’ of Neo-Confucianism and the re-formation of the Confucian scholarly transmission”—which invoked a more inclusive view of true Confucianism. We need, first, to break out of the narrow view of Qing scholars as limited to evidential studies, and second, to revise the emphasis on Qing statecraft that ignores the pure scholarship of Qing Confucians. More importantly, Qing Confucians enlarged the entire field of knowledge as they developed and reflected on traditional scholarship, and the period saw the start of the autonomy of particular branches of knowledge. This article broaches the topic through an examination of three institutions and their significance for Qing scholarship. First, the reform of the Confucian Temple. How did the academic community starting in the early Qing work to reinstall classical scholars of the earlier tradition into the Temple? The key figure reinstalled in the Temple was Zheng Xuan, while Qing scholars also thoroughly researched specific Confucian followers and the various schools of Confucianism since the Qin-Han in a reworking of scholarly genealogies. Second, the efforts of the Han Learning school in the Qianlong and Jiaqing periods to establish the Duke of Zhou, Fu Sheng, and Zheng Xuan as “Erudites of the Five Classics” (五經博士). These efforts proved to be of great significance to changes in scholarship, including a specialized methodology of the Han Learning school as seen in the rise of the analyses of historical texts, institutions, and the Shuowen dictionary—as opposed to the Neo-Confucian school’s emphasis on “morality and principle.” And third, sacrifices marked a new sense of the “scholarly transmission” in academic circles. The Gujing Academy established a Temple to Xu Shen and Zheng Xuan in the Jiaqing period, not found in other academies at the time, but the idea had spread widely by the Guangxu period, when new genealogies defined the transmission of the classics from the Han to the Qing, and sacrifices to Xu and Zheng followed the form of Confucian Temple sacrifices. Halls for Respecting the Classics were founded in many localities, and the anniversary of Zheng Xuan’s birthday was even celebrated like that of Confucius. The effects of Confucian scholars to rework the scholarly transmission—at a time when the Qing emperors claimed to fill the position of Yao and Shun and to personally manifest the transmission of the Way and of legitimate rulership—demonstrate that scholarly circles were already constructing an autonomous sense of scholarly transmission outside of the traditional ideology that linked politics and learning. “Not the orthodox transmission of the Way but finding the Way in learning” was the key to their understanding. This self-aware academic movement had two further features: first, we can see that Qing Confucians greatly developed the resources of traditional scholarship, thus creating more multifaceted forms of knowledge; and second, they were reevaluating the content and value of traditional scholarship.