Our multi-level capital market has began to be shaped，the OTC market is booming and growing rapidly，the corporate governance structure of SMEs has been continuously improved. At the same time，“board of directors、board of supervisors and general meeting” running nonstandard，rights of small shareholders and other stakeholders being infringed，and selective disclosure and lag problems of information gradually emerged，seriously hampered the healthy development of SMEs in the OTC market. From the basic theory of corporate governance，we start to focus on the present situation and the reasons for the OTC market SMEs’ corporate governance，discuss in details about the uniqueness of the OTC market for SMEs，and the reasons for the problems，finally we put forward some specific recommendations from both internal governance and external governance angle.