Abstract: At present, medium-small enterprises (MSEs) play an important role in developing the nation economy. And the innovation is the key of MSEs to keep the core competition capacity and surviving in the intense competition. Therefore, this study would explore the decisive indicators of independence innovation in MSEs with factor analysis. The result suggests there are eight factors influencing the independence innovation in MSEs, i.e., firm size, research and development (R&D), innovation environment, innovation extent, technology conversion, innovation incentive, intellectual and compensation. The larger is the enterprise, the more innovative activities there are in MSEs. The remained factors also have significant effects on the independence innovation in MSEs. These eight main factors can interpret 79% of independence innovation in MSEs. Therefore, we should strengthen these eight aspects in order to maintain the independence innovation in MSEs.