In order to improve the innovation capability of manufacturing industry of Anhui province, based on the strategy of“Made in China 2025”, this paper analyzes the present situation of innovation in Anhui's manufacturing industry from the overall development situation, innovative investment and output, which reflected in the large gap in the scientific and technological institutions, scientific and technological activities and human resources investment, and manufacturing industry when comparing with developed regions, as well as the low conversion rate of innovation achievements and weak output capacity. Then, the author points out the development difficulties in Anhui manufacturing industry, such as unsound innovation system, insufficient innovation investment, lack of innovation talents, and weak product quality and brand building, therefore, the author puts forward suggestions to promote the construction of innovation system, improve the independent innovation ability of enterprises, strengthen the development of innovative talents, and enhance the quality and brand building.