The targeted funding model of universities is a concrete practice that embodies the idea of "targeted poverty alleviation". It provides new method and concept to enhance the accuracy of universities' poverty alleviation. Big data technology has significant advantages for the collection and analysis of information,which will be effective to provide adequate information for sponsors,to provide evidences of facts for diversified forms of poverty alleviation,as well as to provide technical conditions to improve effectiveness. In order to achieve the goal of optimizing targeted funding model of universities,under the guidance of the system theory,it should focus on the integrity of the system,and emphasize the internal coordination. The paper constructed a frame and made institutional innovation in four fields,including framework design,system guarantee,technical path and linkage mechanism.