Prenatal opioid exposure has been linked to adverse effects spanning multiple neurodevelopmental domains, including cognition, motor development, attention, and vision. However, the neural basis of these abnormalities is largely unknown. A total of 49 infants, including 21 opioid-exposed and 28 controls, were enrolled and underwent MR imaging (43 ± 6 days old) after birth, including resting state functional MRI. Edge-centric functional networks based on dynamic functional connections were constructed and machine-learning methods were employed to identify neural features distinguishing opioid-exposed infants from unexposed controls. An accuracy of 73.6% (sensitivity 76.25% and specificity 69.33%) was achieved using 10 times ten-fold cross-validation, which substantially outperformed those obtained using conventional static functional connections (accuracy 56.9%). More importantly, we identified that prenatal opioid exposure preferentially affects inter- rather than intra-network dynamic functional connections, particularly with the visual, subcortical and default mode networks. Consistent results at the brain regional and connection levels were also observed, where the brain regions and connections associated with visual and higher order cognitive functions played pivotal roles in distinguishing opioid-exposed infants from controls. Our findings support the clinical phenotype of infants exposed to opioids in utero and may potentially explain the higher rates of visual and emotional problems observed in this population. Finally, our findings suggested that edge-centric networks could better capture the neural differences between opioid-exposed infants and controls by abstracting the intrinsic co-fluctuation along edges, which may provide a promising tool for future studies focusing on investigating the effects of prenatal opioid exposure on neurodevelopment.