<p>Partial Boolean algebra underlies the quantum logic as an important tool for quantum contextuality. We propose the notion atom graphs to reveal the graph structure of partial Boolean algebra for finite dimensional quantum systems by proving that (i) the partial Boolean algebras for quantum systems are determined by their atom graphs; (ii) the states on atom graphs can be extended uniquely to the partial Boolean algebras, and (iii) each exclusivity graph is an induced graph of an atom graph. (i) and (ii) show that the finite dimensional quantum systems are uniquely determined by their atom graphs. which proves the reasonability of graphs as the models of quantum experiments. (iii) establishes a connection between atom graphs and exclusivity graphs, and introduces a method to express the exclusivity experiments more precisely. We also present a general and parametric description for Kochen–Specker theorem based on graphs, which gives a type of non-contextuality inequality for KS contextuality.</p>