The period of endocrine regulation during the late gestation stage is crucial for the establishment of the neonatal hormonal homeostasis, but it is also the most susceptible to systemic endocrine disruption. This research focused on the integrated hormonal profile of the mother, placenta, and neonatal, to determine the impact of perturbed late gestation endocrine on neonatal hormone imbalance. The surface and multivariate analyses show nonlinear and threshold-dependent associations of maternal endocrine disruption and the neonatal imbalance of cortisol and thyroid and the metabolic hormones, suggesting that there is a finite capability of the placenta to buffer. The multivariate and the stratification analysis showed a coordinated dysregulation of the system of stress, metabolism, and the growth hormones. Moreover, the predictive analytics showed that the late gestation endocrine profile is an accurate predictor of the neonatal hormonal dysregulation risk. These results emphasize the role of the placenta, under chronic endocrine disruption, is as a critical hormonal buffer and a failure point. Hence, the Endocrine disruption, under the chronic stress of the system, is a critical gestational stressor, with direct effect to the newborn. These results highlight the value of the risk stratification based on endocrine markers for predictive neonatal care and the management of the perinatal hormonal regulation.