Although the research on crisis and crisis management has experienced for more than 20 years, the business enterprise crisis did not happen less, and rather become more frequent and serious. The reason is of not deeply investigating the nature of the crisis. This paper analyses the nature of the business enterprise crisis in the level of relationship between the ecosystem of business enterprise and the business enterprise, and it presents the idea that the nature of the crisis in modern business enterprise consists in the essential flaw of its institution system.