The transformation efficiency of scientific and technological （S&T） achievements in China is low，and it is urgent to build a standardized management system with clear logic， complete system and effective practice. Based on the national innovation system theory， it analyzed the function position of colleges in national innovation system， and focused on the problems， such as the management of resources lack of effective integration， the process lack of effective supervision and control， and the distribution of achievements lack of powerful system. It put forward the concept and system structure of transformation of S&T achievements management system of colleges ， and divided the management system of S&T achievements transformation into innovation factor input system， innovation process management system and innovation achievement distribution system. The conclusion provides theoretical support for the transformation management of S&T achievements in colleges， and puts forward the theoretical or practical improvement direction that should be paid attention to in the future.