In B2B e-commerce environments, many initiatives for process modeling have made efforts to design business processes correctly. Especially, Petri nets have been widely used as a good theory to design and verify process models. Therefore, we propose the process modeling method for the B2B e-commerce based on Petri nets. First of all, a B2B process model based on BPSS is represented by the UML activity diagram. Second, the activity diagram is transformed to a Petri net model. For the transformation, well-behaved building blocks/control structures and the modeling rules for inter-organizational workflow processes are proposed. Third, the process is partitioned into sharable processes for individual business partners. Finally, according to needs of individual business partners, the sharable processes are modified by well-structured refinement rules. The whole procedure is explained with the purchase process of an e-bookstore.