Party organizations at the primary level play a leading role in modernization of the internal governance system in universities and the governance capability thereof, it is necessity to further the research on the way to improve the organizational power of the primary Party organizations from the perspective of governance modernization. It is find that new challenges are posed by the modern governance in terms of initiative of subjects, tolerance of values, fairness of the system, and equal opportunity of practice and so on. To meet these challenges, five transformations should be in place to improve the organizational power, including transforming the attribute expression from “knowing” into “identifying with”, the concept of practice from “management” into “governance”, the subject of practice from “single” into “plural”, the working mechanism from “connecting” into “coupling”, and the evaluation mechanism from “separating examination from application” into “integrating examination with application”.