The time-to-market pressure and continuous growing complexity of hardware designs have promoted the globalization of the Integrated Circuit (IC) supply chain. However, such globalization also poses various security threats in each phase of the IC supply chain. Although the advancements of Machine Learning (ML) have pushed the frontier of hardware security, most conventional ML-based methods can only achieve the desired performance by manually finding a robust feature representation for circuits that are non-Euclidean data. As a result, modeling these circuits using graph learning to improve design flows has attracted research attention in the Electronic Design Automation (EDA) field. However, due to the lack of supporting tools, only a few existing works apply graph learning to resolve hardware security issues. To attract more attention, we propose HW2VEC, an open-source graph learning tool that lowers the threshold for newcomers to research hardware security applications with graphs. HW2VEC provides an automated pipeline for extracting a graph representation from a hardware design in various abstraction levels (register transfer level or gate-level netlist). Besides, HW2VEC users can automatically transform the non-Euclidean hardware designs into Euclidean graph embeddings for solving their problems. In this paper, we demonstrate that HW2VEC can achieve state-of-the-art performance on two hardware security-related tasks: Hardware Trojan Detection and Intellectual Property Piracy Detection. We provide the time profiling results for the graph extraction and the learning pipelines in HW2VEC.