Microfinance institutions (MFIs) play an significant role in financial inclusion and poverty alleviation activities. A critical challenge facing MFIs is how on all to build its own capacity for sustainable and healthy development. By using the data from the pilot survey of 65 microcredit companies in Zhejiang of China, this paper explores the factors affecting MFIs activities by principal component analysis and analyzes the key Influencing factors and sustainable development performance with the analysis of variance and multi-regression model.The results indicate that four key factors of operational technology, external environment, financial condition and institution size have a significant positive effect on the economic sustainability performance of MFIs, while the adjusted institution size is insignificant positive effect on operational sustainability performance,which means that key factors of MFIs sustainability have a greater impact on economic sustainability performance than operational sustainability performance.