Abstract: The meaning of collaborative innovation of cross-strait agricultural science and technology was discussed in this paper and its connotation was scientifically defined. Then, based on the theories of synergetics and Triple Helix, the theoretical basis of collaborative innovation of cross-strait agricultural science and technology was elaborated. In addition, by combining the theory and practice, the SWOT analysis of collaborative innovation of cross-strait agricultural science and technology was carried out, and then the corresponding targeted development strategies were put forward.