Childhood neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), attention-deficit hyperactivity disorder, and Tourette syndrome, are a predominant cause of health-related disabilities in children and adolescents. Nevertheless, disease biomarkers are still limited. The aim of this study was to evaluate the potential, causal relationship between mitochondrial DNA copy number (mtDNA-CN), metabolic disorders, and childhood NDDs using the two-sample Mendelian randomization (MR) method. Genetic associations with mtDNA-CN, disorders of lipoprotein metabolism, and disorders of iron metabolism were selected as exposures, and genome-wide association data from ASD, attention-deficit hyperactivity disorder, and Tourette syndrome were utilized as outcomes. Results of the study suggested that a high degree of disordered lipoprotein metabolism related increases in ASD risk result from a decrease in mtDNA-CN (disordered lipoprotein metabolism-mtDNA: inverse variance weighting beta: -0.03, 95% confidence interval: -0.05 to -0.02, P = 2.08 x 10-5; mtDNA-CN-ASD: inverse variance weighting odds ratio: 0.83, 95% confidence interval: 0.69-0.99, P = .034). The research findings implied that mtDNA-CN can mediate disorders of lipoprotein metabolism, potentially influencing the development of ASD. The potential impact of the results of this study for the prevention and treatment of childhood NDDs warrants validation in robust randomized clinical trials.