Most cancer-related deaths come from metastasis. It was recently discovered that nanoparticles could inhibit cancer cell migration. Whereas most researchers focus on single-cell migration， the effect of nanoparticle treatment on collective cell migration has not been explored. Collective migration occurs commonly in many types of cancer metastasis， where a group of cancer cells move together， which requires the contractility of the cytoskeleton filaments and the connection of neighboring cells by the cell junction proteins. Here， we demonstrate that gold nanorods (AuNRs) and the introduction of near-infrared light could inhibit the cancer cell collective migration by altering the actin filaments and cell junctions with significantly triggered phosphorylation changes of essential proteins， using mass spectrometry-based phosphoproteomics. Further observation using super-resolution stochastic optical reconstruction microscopy (STORM) showed the actin cytoskeleton filament bundles were disturbed， which is difficult to differentiate under a normal fluorescence microscope. The decreased expression level of N-cadherin junctions and morphological changes of tight junction protein zonula occludens 2 were also observed. All of these results indicate possible functions of the AuNR treatments in regulating and remodeling the actin filaments and cell junction proteins， which contribute to decreasing cancer cell collective migration.