The scientific achievement transformation of collaboration innovative center is an advanced question. On the one hand, the current proportion of scientific research achievements transformed into productivity in our country and in universities is low. The main reason is the rigid scientific system and the laggard development. On the other hand, according to the 2011 plan, collaboration innovative centers based on universities are good for the current scientific system in the design of scientific system. Therefore, research on the scientific achievement transformation of collaboration innovative centers is beneficial for the transformation of scientific system in universities. In the present paper, we firstly explained briefly the concept of collaboration innovative center and then analyzed the main difficulty in the scientific achievement transformation of collaboration innovative centers in universities. We also analyzed the structure of collaboration innovative centers and indicated that collaboration is its essential idea. Finally, we put forward several working points in the system of scientific achievement transformation of collaboration innovative centers.