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This study investigated whether diffusion tensor imaging tractography-based connectome can differentiate global developmental delay from speech delay in young children. Twelve children with pure speech delay, 14 children with global developmental delay, and 10 children with typical development underwent 3T DTI. Whole-brain connectome analysis was performed by using 116 cortical ROIs. Network metrics were measured at individual regions: strength, efficiency, cluster coefficient, and betweeness. Compared with typical development, global and local efficiency were significantly reduced in both global developmental delay and speech delay. Nodal strength of the cognitive network was reduced in global developmental delay, whereas the nodal strength of the language network was reduced in speech delay. This finding resulted in a high accuracy of >83% to discriminate global developmental delay from speech delay.