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Graph‐theoretical methods have revolutionized the exploration of complex systems across scientific disciplines. Here, we demonstrate their applicability to the investigation and comparison of three widely used atmospheric chemical mechanisms of varying complexity: the Master Chemical Mechanism v3.3, GEOS‐Chem v12.6, and the Super‐Fast chemical mechanism. We investigate these mechanisms using a class of graphical models known as species‐reaction graphs and find similarities between these chemical reaction systems and other systems arising in nature. Several graph theoretical properties are consistent across mechanisms, including strong dynamical system disequilibrium and clustering of chemically related species. This formalism also reveals key differences between the mechanisms, some of which have characteristics inconsistent with domain knowledge; e.g., isoprene and peroxy radical chemistry exhibit substantially different graph properties in each mechanism. Graph‐theoretical methods provide a promising set of tools for investigating atmospheric chemical mechanisms, complementing existing computational approaches, and potentially opening new avenues for scientific discovery. Plain Language Summary: A type of math known as "graph theory" provides a set of tools for scientific discovery in a variety of contexts. These include the study of social networks, the power grid, and the human brain. In this paper, we apply these tools to the study of the chemical reactions that occur in the atmosphere. We investigate and intercompare several different descriptions of these reactions, and find that these new graph theory‐based techniques provide information consistent with existing scientific techniques, and potentially allow for new avenues for scientific discovery. Key Points: We investigate three atmospheric chemical mechanisms of varying complexity and process representation using graph‐theoretical techniquesResults are consistent with existing computational approaches, demonstrating key similarities and differences between the mechanismsThese techniques provide chemical state independent, structural insights into existing mechanisms, and methods for new mechanism development [ABSTRACT FROM AUTHOR]