Two-dimensional (2D) van der Waals (vdW) materials offer rich tuning opportunities generated by different stacking configurations or by introducing intercalants into the vdW gaps. Current knowledge of the interplay between stacking polytypes and intercalation often relies on macroscopically averaged probes, which fail to pinpoint the exact atomic position and chemical state of the intercalants in real space. Here, by using atomic-resolution electron energy-loss spectroscopy in a scanning transmission electron microscope, we visualize a stacking-selective self-intercalation phenomenon in thin films of the transition-metal dichalcogenide (TMDC) Nb₁₊ₓSe₂. We observe robust contrasts between 180°-stacked layers with large amounts of Nb intercalants inside their vdW gaps and 0°-stacked layers with little detectable intercalants inside their vdW gaps, coexisting on the atomic scale. First-principles calculations suggest that the films lie at the boundary of a phase transition from 0° to 180° stacking when the intercalant concentration x exceeds ~0.25, which we could attain in our films due to specific kinetic pathways. Our results offer not only renewed mechanistic insights into stacking and intercalation, but also open up prospects for engineering the functionality of TMDCs via stacking-selective self-intercalation.
