Pipe diffuser can adapt the high Mach number distorted flow in high pressure ratio centrifugal compressors because of its special scallop leading edge. However, the special leading edge could generate pair vortices and it is not clear if the pair vortices have positive or negative effect on pipe diffuser performance. Besides, the generation and development of pair vortices are also need to be investigated. This work is aimed at uncovering the influence of vortices on aerodynamic loss in pipe diffuser. Pipe diffusers with several different geometries are designed for a high pressure ratio centrifugal compressor used in a small gas turbine. The generation and evolution of pair vortices in pipe diffuser passages are studied by validated state-of-the-art CFD method. Detailed understandings of the influence of different geometries on pair vortices and pipe diffuser performance are provided. Through these works, it is found that the pair vortices could enhance the flow mixing of high and low energy flow in pipe diffuser passage near throat, thus the boundary layer becomes thin, and the flow separation is suppressed near pipe diffuser throat under large negative incidence. However, pair vortices also move low momentum flow to the pressure side and induced separation in pipe diffuser cone after throat, eventually. The diffuser inlet-to-impeller exit radius ratio and diffuser cross section shape could affect the compressor performance by changing the intensity of pair vortices. The diffuser with inlet-to-impeller exit radius ratio 1.02 and the pipe diffuser with the cross section with big fillets such as 3.37 mm are recommended for their good performance. The diffuser throat area and passage count can also have impact on pair vortices, but the compressor performance is not only influenced by pair vortices when these two parameters are changed.