In supply chain management system there are a large number of event logs recording the performers who initiate or complete the activities. Virtual organization structure is so flexible as to be more suitable for supply chain management. However the existing organizational structure modeling methods are difficult to model virtual structure. This paper design an automatic modeling method of virtual organization structure based on event logs from SCMS. Firstly, six kinds of performer relations are analyzed, i.e. PR1-PR6; Secondly, Five kinds of modeling rules are designed, i.e. MR1-MR5; At last, an actual case are given to verify feasibility of this method.