The nonlinear dynamic innovation process can be realized through the triple helix collaborative innovation mechanism of medical universities, pharmaceutical enterprises and government. The medical virtual research and development organization can be divided into three modes, including the government led mode, medical university pushed mode and pharmaceutical enterprises draw mode. The medical university-industry- government collaborative innovation virtual research and development organization has the advantages of the fuzzy organization boundary, the flat organization structure and the flexibility of the organization structure, which can guarantee the cooperation of the triple helix collaborative innovation. The external policy support and effective inner management of the organization should be applied to realize the collaborative innovation of virtual medical research and development organization.