BACKGROUND: Dietary cystine may influence lipid metabolism, but epidemiological evidence in children is limited. This study aimed to investigate the association between dietary cystine intake and dyslipidemia and its subtypes in Chinese children. METHODS: Data were derived from the China National Nutrition and Health Surveillance of Children and Lactating Mothers (CNNHSCLM). After propensity score matching (1:1, caliper = 0.2), 3676 children aged 6-17 years (1838 with dyslipidemia, 1838 controls) were included. The Quantile g-computation (qgcomp) model assessed the joint effect of 20 amino acids. Multivariate logistic regression, subgroup analysis, restricted cubic splines (RCS), and five machine learning models (including XGBoost with Shapley Additive Explanation (SHAP) analysis) were applied to evaluate the association between cystine intake and dyslipidemia. RESULTS: The qgcomp model showed that cystine had a negative weighting contribution to reducing the risk of hypo-HDL cholesterolemia. Multivariate logistic regression revealed that cystine intake was significantly negatively correlated with hypo-HDL cholesterolemia (OR = 0.67, 95%CI: 0.53-0.86, p = 0.002) and total dyslipidemia (OR = 0.84, 95%CI: 0.74-0.96, p = 0.010), but not with other subtypes. Subgroup analyses indicated interactions with BMI and sex. RCS showed a non-linear dose-response relationship for hypo-HDL cholesterolemia and a linear negative relationship for total dyslipidemia. The XGBoost model achieved the best predictive performance (AUC = 0.902), and SHAP analysis identified cystine as the most important feature inversely associated with dyslipidemia. Decision curve analysis confirmed its clinical net benefit. CONCLUSIONS: Dietary cystine intake is negatively associated with the risk of hypo-HDL cholesterolemia and total dyslipidemia in children, and cystine is an important negative correlate of dyslipidemia. These findings provide new scientific evidence for dietary prevention of dyslipidemia in children.