Abstract: Objective To understand the epidemic of suicide ideation among less-populated ethnic students in primary and junior schools of China, to identify the risk factors of suicide ideation, and to provide scientific evidence for developing strategy and health policies to intervene their suicide-related behavior among ethnic minorities. Methods Less-populated ethnic students, aging between 9 and 16 years old, were recruited. Randomized cluster sampling was adopted. A self-designed questionnaire was used to collect data. Risk factors for suicide ideation were assessed by univariate analysis and Logistic regression analysis. Results In 2016, 16.38%(430/2 625) of the less populated ethnic students in primary and junior school students of China had suicide ideation during the past 12-month period prior to the study, of which, the incidence was 17.39% in boys and 15.44% in girls. When stratified by ethnic groups, the self-reported incidence of suicide ideation among students in different ethnic groups was significantly different. The incidence rate was 16.80% among Bulang people, 13.43% among Achang people, 14.64% among Pumi people, 33.52% among Nu people, 11.70% among De'ang people, 11.71% among Dulong people, and 13.44% among Jinuo people. The multi-variates logistic regression analysis showed that students who had self-injury events, and unintentional injury over the past 12 months, felt lonely, stopped their daily activities continuously for two weeks or longer due to depression, suffered school violence over the past 30 days, were left-behind children, had mothers engaged in non-agricultural work, or had lower educational level in parents were more likely to have the idea of suicide. Conclusions The problem of suicide ideation cannot be ignored among the less-populated ethnic students in primary and junior school students of China. In the future, we should strengthen the prevention and comprehensive intervention against suicide related behavior in primary and middle school with more ethnic students.