Background: A significant association between self-harm (SH) and suicide ideation (SI) has been found in Chinese left-behind children (LBC). Existing literature suggests that resilience might be a mediator in this association. However, this hypothesis has not been effectively discussed. The major aim of our study is to analyze the possible mediation of resilience in SH-SI association in Chinese LBC. Methods: A population-based clustering sampling survey of 2619 LBC was conducted in southwestern China Yunnan province. Self-developed structured questionnaire was used to collect relevant information. Univariate and multivariate Logistic regression models were applied to estimate the associations between SH and SI, resilience and SI, and SH and resilience. Path analysis was adopted to measure the mediation of resilience, as well as its 5 dimensions, in the association between SH and SI. A subgroup analysis was further done to explore the mediation of resilience in the associations between SH severity and SI, SH repetition and SI, among self-harmed LBC. Results: Compared with LBC who reported no SH behaviors, the odds ratio (OR) for SI was 3.37 (95% CI: 2.63–4.31) among self-harmed LBC. Based on the path model, resilience significantly mediated a quarter of the total association between SH and SI. Among the 5 dimensions of resilience, emotion regulation, interpersonal assistance, and family support were the strongest mediators. Subgroup analysis revealed that, the mediation of resilience was only significant for SH severity and SI. Conclusions: Resilience played as a prominent mediator in SH-SI association among Chinese LBC. Resiliencecentered intervention measures could be considered to reduce suicidal risk of this disadvantageous group.