The response to extreme natural disasters needs to focus on concentration and mobilization of all sorts of national forces and resources which requires a strong unified emergency command organization to command and coordinate. To this end, emergency command organization structure (ECOS) is essential in standardizing establishment of emergency command organization. Aiming at the problem that unclear responsibilities and incoherent relationships among members with various organization structures hinder rapid joint action and collaboration in emergency response process, an open and rational ECOS (ORECOS) based on organization theory is presented. A case study of ECOS of Three Gorges flood control is made to demonstrate and verify the applicability and rationality of ORECOS, taking Three Gorges suffered Yangtze River whole basin-wide flood in 2010 as background. The results show that the whole ORECOS based on matrix structure consists of three components: administrative emergency response system (AERS) based on bureaucratic structure, area commands (ACs) based on project team structure and consultation groups (CGs) based on task force structure. With a combination of rigidity, flexibility, hierarchy, authority, openness and contingency, ORECOS is more suited to China's national conditions and can create more effective emergency responses to extreme natural disasters.