Abstract: The innovation process of the modern bio-technology is characterized by “relay innovation”, meanwhile, the operation of the intellectual property rights is especially important to the relative enterprises. During the process of the relay innovation, the expert company and the core company will choose different relay modes based on the different stage and timing of the innovation. On the basis of the existing research, taking the bio-pharmaceutical enterprises as example, it discusses thoroughly the different operation modes of the intellectual property rights of the expert company and the core company under the different ways of relay cooperation. We are looking forward to providing effective references to the modern bio-technology enterprises in China for the intellectual property rights management and practice.