This paper is an attempt to search for a meta-theoretical foundation to an integrated Korean studies. Without its own target and methodology, it will be difficult for Korean studies to be established as an independent academic discipline. In particular, the antagonism of the ‘Two Cultures,’ referring to the juxtaposition between humanities and the sciences, has been reproduced into a humanities-based ‘National studies’ (‘國學’) and a social science-based ‘Korean studies’ (‘韓國學’), and is acting as a factor preventing a more holistic perspective of Korean society. Such division originated from the modern academic disciplinary structure systemized at the end of the 19th century but was then deepened by the path dependency of the division system and the external dependency of the Korean academia. Under this context, this paper seeks to graft critical naturalism of Marx and Durkheim, who envisioned unified sciences at the end of the 19th century, before separation into modern academic disciplines took place, to the attempts to alleviate the ‘Two Cultures’ and thereby project an integrated Korean studies. Critical naturalism of the two thinkers – in particular, their relational social paradigm and theory of explanatory critique – proposes a third way that resolves the dichotomies between society and people, science and philosophy, nomothetic and idiographic methods, and facts and values, thus positioning itself as a paradigmatic basis for unified knowledge that overcomes the antagonism between hyper-naturalist positivism and anti-naturalist humanities. Moreover, the critical naturalism of the two provides the possibility of depth-explanatory human sciences that integrates the historicity and the scientificity of a divided society as well as abundant philosophy of science resources to promote a more complete Korean studies that encompasses both the South and the North.