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Background: Intellectual developmental disorders are a serious source of health morbidity with negative consequences for adults as well as children. However, there is limited evidence on the environmental, trace element, behavioural, and emotional outcomes in children. Here, we investigated whether there is any association between child behaviour and emotional outcomes and micronutrients using network analysis. Methods: A cross-sectional study was conducted in 9-year-old children within a Pacific Island Families study birth cohort. Elemental concentration was determined in children’s toenails after acid digestion and analysed using inductively coupled plasma mass spectrometry. We used network analysis to identify closely associated trace elements and tested the directions and strength of these trace elements. MANCOVA were used to identify the significant associations between individual elements and the behavioural/emotional function of the children using the children behaviour checklist (CBCL). At the final step, quantile regression analysis was used to assess and quantify the identified associations between CBCL function scores and manganese, adjusted by sex, ethnicity, and standardized BMI. Results: Three major nutrient networks were identified. In the Mn network, Mn was strongly positively associated with Al (0.63) and Fe (r = 0.65) and moderately associated with Pb (r = 0.45) and Sb (r = 0.42). Al was also strongly associated with Fe (r = 0.9). Children in the second or third clinical group, with an elevated externalized CBCL score, had a much higher mean and median level of Mn as compared to the normal range group. The aggression score was significantly associated with Mn concentration and sex. Higher Mn concentrations were associated with a higher aggression score. A 1 ug/g unit increase in Mn was associated with a 2.44-fold increase (95% confidence interval: 1.55–4.21) in aggression score, and boys had higher median aggression score than girls (difference: 1.7, 95% CI: 0.9–2.8). Attention and rule breaking scores were both significantly associated with Mn concentration. Higher Mn concentrations were associated with higher attention behaviour problem and rule breaking scores. A 1 ug/g unit increase in Mn was found to be associated with a 1.80-fold increase (95% confidence interval: 1.37–2.82) in attention score, and a 1.46-fold increase (95% confidence interval: 1.01–1.74) in the rule breaking score. Thought score was not significantly associated with Mn concentration (p = 0.13) but was significantly lower in boys (p = 0.004). Conclusions: Exceeding Mn levels is potentially toxic and has been identified to be associated with worse externalized children’s behavioural health and emotional well-being. Future studies are necessary to find the exposure paths so that advice shall be provided to family and care providers in public health and environmental protection.