This study assumes the rising diplomatic disputes between South Korea and China over the ethnic Koreans in China are due to the difference in bilateral perceptions. In order to examine the difference closely, it surveyed research institutes, scholars and their trends of the Chinese Koreans Studies in South Korea and China comparatively. It collected data from field-work researches and interviews in Beijing and Seoul as well as from various on-line resources. Through the survey, it revealed that the difference comes with distinct research interests and prospects of the Chinese Koreans issue in the two countries, and that the difference are due to their distinct structural backgrounds. That is, the fact that Korea has been an uni-ethnic country while China has been a multi-ethnic country leads to the different perceptions. This study also emphasizes that the ethnic Koreans in China should not be regarded as a by-product of the political relationship between South Korea and China, but they should be rather regarded as an independent group of people with their own identity and purpose for existence between the two countries.