MOTIVATION: Revealing structural variations within and across populations is crucial for understanding their diversification mechanisms and roles. Existing tools for visualization of structural variations often require labor-intensive figure preparation and are limited in their ability to integrate annotations. RESULTS: We developed PatchWorkPlot, a tool for automated visualization of pairwise alignments of multiple annotated sequences as dot plots combined into a single matrix. PatchWorkPlot enables exploration of positions, breakpoints, and architectures of structural variations across two or more sequences. The tool supports customization of visualization parameters and produces high-resolution, publication-ready figures. PatchWorkPlot significantly reduces manual work and simplifies the generation of complex plots for various cases, from individual loci to large-scale comparative projects. AVAILABILITY AND IMPLEMENTATION: PatchWorkPlot is implemented using Python 3 and is publicly available at GitHub: github.com/yana-safonova/PatchWorkPlot.