Non-traditional security has become an important issue of international security issues, and is also facing a threat to cross-strait relations. If it is the connotation of military facets of cooperation (agreement) to facilitate the development of the cross-Strait relations, it also reduces the doubts surrounding countries. Therefore, the proposal of this thesis has focused on the non-traditional security. This research has primarily focused on non-traditional security fields including disaster prevention, disease control and sea rescue to explore current cross-strait cooperation model. Further, this study discussed future research on construction of security cooperation mechanism, and analyzed the cross-strait military security in response to the law of non-traditional sources and strategies. The result of this research found that cross-strait exchange in the dispute over sovereignty is the main constraining factor. Both in response to non-traditional security threats related to resources have not yet integrated to build the mechanism of security cooperation, and play an important role in the military are cross-strait to toward the future. In addition, the conclusion of this research indicated that cross-strait should build a non-traditional security through academic exchange, channels of negotiation, friendly reciprocal visits, and joint exercises of compound disaster, and the inclusion of cross-strait military security cooperation mechanism within policy formation process.