Goal-oriented dimension is a new angle to solve the problem of universities’ performance assessment. Firstly, designs an input-output index system, and calculates the Malmquist Index of the performance utilizes the panel data. Then, the non-parametric KDE graph is used in this research for further discussion of the differences of TFP changes. Meanwhile, a non-parametric KDE analysis is carried out respectively for TECHCH, EFFCH, PTEC, and SECH indexes. The Malmquist-KDE index model shows the results as follows: TFP is on a declining curve; the increased range of EFFECH is relatively smaller, while the annual growth of PECH and SECH are slow; the decrease of TFP is caused by the decrease of TECHCH; the general distribution gradually moves leftward, reflecting a fact that the TFP changes are decreasing progressively; the TFP change rate demonstrates obvious a skewed distribution; the patterns in the graph gradually shift from thin and tall ones into short and thick ones. Conversely, the changes of external factors force universities to improve their operations actively.