With the rapid development of Chinas new OTC market，the financing channels for small and medium sized enterprises have been broadened accordingly.The financing efficiency in the new OTC market also attracts much attention.This paper makes a comparative study on the financing efficiency of the three stage DEA model.Results show that eliminating the environmental variables and adjusting the input value after the measurement of the efficiency of the third stage can accurately reflect the financing efficiency of the new OTC enterprises.The low financing efficiency of small and medium sized enterprises in the new OTC market is mainly affected by the low scale efficiency caused by the unreasonable input and output.