Staying in the U.S., Cheon was a postdoc in the University of California Berkeley. For the next three years, he was a staff research associate at UCLA before returning to Korea to work as an assistant and then associate professor at KAIST. His research at KAIST focused on geometrical shape control of nanoparticles and magnetic particles. This also marked his first publication on nanocrystals which is a reoccurring interest in his research career and a source of multiple highly cited articles.
He started working at Yonsei University as a full professor in 2002 and later became the Horace G. Underwood Professor in 2008. His research at Yonsei on nanoscale phenomena has led to nanomaterial applications in biology, including highly sensitive MRI contrast agents and  nanoscale toolkits for cells. A notable study is from 2004, when he demonstrated the principle of size-dependent MRI contrast effects using nanoparticles which enabled the development of magnetism-engineered iron oxide (MEIO) as an ultra-sensitive nanoparticle MRI contrast agent which might help detect early stage cancer.
From 2010 to 2016, Cheon was the director of the National Creative Research Initiative Center for Evolutionary Nanoparticles. From 2015, he became the director of the newly established Yonsei-Institute of Basic Science Center for Nanomedicine at the Yonsei University Sinchon campus.