Molecular-scale understanding of rheological properties of small-molecular liquids and polymers is critical to optimizing their performance in practical applications such as lubrication and hydraulic fracking. We combine nonequilibrium molecular dynamics simulations with two unsupervised machine learning methods: principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), to extract the correlation between the rheological properties and molecular structure of squalane sheared at high strain rates (106–1010s−1) for which substantial shear thinning is observed under pressuresP∈0.1–955 MPa at 293 K. Intramolecular atom pair orientation tensors of435×6dimensions and the intermolecular atom pair orientation tensors of61×6dimensions are reduced and visualized using PCA and t-SNE to assess the changes in the orientation order during the shear thinning of squalane. Dimension reduction of intramolecular orientation tensors at low pressuresP=0.1,100MPa reveals a strong correlation between changes in strain rate and the orientation of the side-backbone atom pairs, end-backbone atom pairs, short backbone-backbone atom pairs, and long backbone-backbone atom pairs associated with a squalane molecule. At high pressuresP≥400MPa, the orientation tensors are better classified by these different pair types rather than strain rate, signaling an overall limited evolution of intramolecular orientation with changes in strain rate. Dimension reduction also finds no clear evidence of the link between shear thinning at high pressures and changes in the intermolecular orientation. The alignment of squalane molecules is found to be saturated over the entire range of rates during which squalane exhibits substantial shear thinning at high pressures.