This paper deals with a new approach to formal reconfiguration of enterprise information system (EIS) flow based on object-based knowledge meshes (OKM) and binary tree. Firstly, information system flow and its corresponding OKM form are discussed. Then the relations between knowledge points are defined, and the approach to structure expression of OKM is proposed, by which the EIS flows can be formally represented. And then, based on the formal representation, EIS flows can be reconfigured according to mapping rules between practical flow and structure expression of OKM. Finally, an order management flow in an EIS is taken as an example to show the feasibility and effectiveness of the approach.