Abstract: Based on the method of exploratory single case study, a typical system-transformed scientific research institute-Northwest Institute(Group) for Non-ferrous Metal Research was chosen, which possesses excellent technical innovation performance in rare metal materials industry in China. The path of pursuing simultaneously both exploitative innovation and exploratory innovation in the process of system transformation was studied.The result shows that: organization differentiation in the process of system transformation possesses typical characteristics of structural ambidexterity, spatial separation not only make exploratory innovation more efficient in organic organization of direct subordinate research institutes, but also ensure that exploitative innovation is more efficient in mechanistic organization of holding companies. Both are supported mutually and integrated organically. The Middle-Phase Links, a key step of transformation from exploratory innovation to exploitative innovation, can resolve effectively the technical and financial risks in the process of industrialization and enhance the success rate of transformation of scientific research. Meanwhile, building the dual network of industry-university-research institute can mitigate the dilemma of resource of ambidexterity innovation and improve the its efficiency in system-transformed scientific research institute.