The morphological fingerprint in the brain is capable of identifying the uniqueness of an individual. However, whether such individual patterns are present in perinatal brains, and which morphological attributes or cortical regions better characterize the individual differences of ne-onates remain unclear. In this study, we proposed a deep learning framework that projected three-dimensional spherical meshes of three morphological features (i.e., cortical thickness, mean curvature, and sulcal depth) onto two-dimensional planes through quasi-conformal mapping, and employed the ResNet18 and contrastive learning for individual identification. We used the cross-sectional structural MRI data of 682 infants, incorporating with data augmentation, to train the model and fine-tuned the parameters based on 60 infants who had longitudinal scans. The model was validated on 30 longitudinal scanned infant data, and remarkable Top1 and Top5 accuracies of 71.37% and 84.10% were achieved, respectively. The sensorimotor and visual cortices were recognized as the most contributive regions in individual identification. Moreover, the folding morphology demonstrated greater discriminative capability than the cortical thickness, which could serve as the morphological fingerprint in perinatal brains. These findings provided evidence for the emergence of morphological fingerprints in the brain at the beginning of the third trimester, which may hold promising implications for understanding the formation of in-dividual uniqueness in the brain during early development.