Nanotechnology is a highly prioritized area on the global scientific agenda. Research into nanotechnology has become part of various scientific disciplines due to its ability to control structures and materials at nanometer scale. This paper analyzes the nanoscientific output of traditional disciplines and their reference citations across disciplines. It attempts to explore the dynamics of nanotechnology research conflation within the nanotechnology system of innovation in Japan. The key factors in nanoscience, technology and innovation management are further studied. Both quantitative and qualitative research methods are adopted, which creates a more solid foundation for exploring the trends in the evolution of this technology. This study offers a useful insight for science and technology policymakers as well as for academic practitioners in science and technical fields in managing the emerging technological systems.