The research method of enterprise accounting system is a system that starting from the overall and then conducting the research of “synthesize-analyze-again synthesize”. Based on this understanding, this paper firstly defined the connotation of enterprise accounting system, then analyzed business flow and combined business flow and enterprise accounting. The conceptual model of enterprise accounting system was constructed based on business flow. The reengineering of accounting enterprise process is the result of market competition and process-oriented flat organizational structure also emerged. This paper broke through the financial accounting principles which was mainly aimed at generating financial statement, and established the traditional thinking of enterprise accounting system. This paper also proposed to establish accounting information system as the primary goal of meeting management demand, thus to enhance the correlation between accounting information and management decision.