Cardiac neural crest cells (CNCCs) contribute to key cardiac structures during embryonic development. Disruption of CNCC patterning or function can lead to congenital heart defects. Here, we investigate whether hemodynamic perturbation alters CNCC behavior in chick embryos. We use the left atrial ligation model to modify intracardiac blood flow in the early common-atrium, common-ventricle heart and track retrovirally labelled CNCCs for lineage tracing and single-cell transcriptomic analysis. Results revealed a significant reduction of CNCC derivatives in major cardiac regions, including the pharyngeal arch arteries and myocardium, in flow-perturbed embryos compared with controls. Notably, despite reduced CNCC numbers in the PAAs, their relative proportion increased, suggesting retention within the PAAs and delayed differentiation. Transcriptional analysis shows the expression of CNCC post-migratory markers (HAND1, FOXC2, GATA6, and TBX2) were consistently downregulated at 4, 24, and 48 hours after LAL. Together, these findings indicate that hemodynamic perturbation impairs CNCC migration and differentiation while preserving their capacity to contribute to mature cardiac structures.