Some thinkers during the Ming-Qing transitional period tended towards monistic thought, which emphasized that li (principle) and qi (material force), xin (heart/mind) and qing (sentiment), and xing (nature) and qing are one rather than two. There were even those proposing extreme arguments that all the conceptual distinctions made by Song-Ming Confucian scholars could be eliminated and all pairs of concepts could be unified. This paper aims to illustrate this kind of thought in terms of its appearance, formation, theoretical meanings, and evaluation. An appropriate understanding of this kind of thought can help not only better interpret the philosophies of individual Confucian scholars, including Wang Yangming, Zhan Ganquan, Luo Zheng’an, Liu Jishan, and Huang Lizhou, but also explain the transformation of Confucianism (a paradigm shift) during the Ming-Qing transitional period. Section one of this paper is an introduction. Section two analyses five different meanings of the thought of oneness in Song-Ming Confucianism and points out that monistic thought is indeed a fault generated by an overemphasis of some meanings of the thought of oneness. Section three investigates the appearance and formation of monistic thought and the final section looks at its influence on the transformation of Confucianism.