Preterm birth is associated with alteration in corticothalamic development, which underlies poor neurodevelopmental outcomes. Our hypothesis was that preterm neonates with CHD would demonstrate abnormal thalamic microstructure when compared to critically ill neonates without CHD. A secondary aim was to identify any association between thalamic microstructural abnormalities and perioperative clinical variables. We compared thalamic DTI measurements in 21 preterm neonates with CHD to two cohorts of neonates without CHD: 28 term and 27 preterm neonates, identified from the same neonatal intensive care unit. Comparison was made with three other selected white matter regions using ROI manual-based measurements. Correlation was made with post-conceptional age and perioperative clinical variables. In preterm neonates with CHD, there were age-related differences in thalamic diffusivity (axial and radial) compared to the preterm and term non-CHD group, in contrast to no differences in anisotropy. Contrary to our hypothesis, abnormal thalamic and optic radiation microstructure was most strongly associated with an elevated first arterial blood gas pO₂ and elevated preoperative arterial blood gas pH (p < 0.05). Age-related thalamic microstructural abnormalities were observed in preterm neonates with CHD. Perinatal hyperoxemia and increased perioperative serum pH were associated with abnormal thalamic microstructure in preterm neonates with CHD. This study emphasizes the vulnerability of thalamocortical development in the preterm neonate with CHD.