Universities 'scientific and technologicalinnovation capacity is an important basis for the evaluationof universities'status and function in national innovationsystem. Its evaluation system and methods need to beperfected. Based on the principal component analysis(PCA) and entropy value method, the evaluation indexsystem of universities ‘scientific and technologicalinnovation capacity is built. The paper takes more than 100universities which belong to 100 key universitiesconstruction project of the 21st century or are sponsored byprovincial government for instance and evaluates theirscientific and technological innovation performance from2009 to 2013. Then the paper puts forwards that the newevaluation system on the basis of the principal componentanalysis and entropy value method can take both theobjective and subjective factors into consideration, which is effective and scientific for the evaluation of universities爷scientific and technological innovation capacity. In order tocope with the unbalanced development of science andtechnology among universities and regions, it proposes thatthe new evaluation system of scientific and technologicalinnovation capacity should use new index of quality factorand should be categorized pertaining to various stages.