Abstract: It was found that quaternions can play an alternative and compact role in surgery navigation system (SNS), to represent rotation. Locating something in different coordinate systems involves the mapping transformation between them. The application of quaternions in the mapping transformation between SNS coordinates and that of spatial registration in SNS are theoretically discussed in detail. The result of simulation shows that the application of quarternions to SNS can solve successfully the two difficult technological problems in SNS, i.e., spatial locating and registration. Both have been used successfully in the SNS model demonstration system NEU-IGSS which was designed and developed by ourselves.