This study proposes a novel partial average fluctuation velocity (PAFV) turbulence based on the PAFV and the average strain rate tensor, which is used to calculate the shock wave boundary layer interaction flows, including cascade flow and transonic compressor flow. In order to illustrate the adequacy, the calculation results of several other turbulence models were also compared with PAFV, including k-ω, shear stress transport, SA-neg (negative Spalart-Allmaras), and stress-BSL (ω-based Reynolds stress model). The suitability of the PAFV turbulence model was initially tested by calculating the transonic flow in the L030-4 cascade. Subsequently, numerical computations were performed for the 3D (three-dimensional) National Aeronautics and Space Administration Rotor 67 transonic compressor rotor. In the numerical simulation, the flow control equations were transformed in a general curvilinear coordinate system for precision enhancement, and the spatial discretization of control equations was executed using the finite difference method. The convection term was processed using the Steger–Warming flux vector splitting method, the diffusion term was discretized using a second-order central difference scheme, and the time derivative term was discretized using the third-order Runge–Kutta method. A parallel computing strategy with multi-block partitioning was employed to speed up the calculations and facilitate faster convergence alongside a local time step method. All numerical computation procedures were written in Python, revealing the following: (1) The PAFV turbulence model aptly simulates the transonic flow within the cascade channel. The shock wave pattern in the cascade channel aligns well with the experimental schlieren images. (2) During the Rotor 67 transonic compressor rotor calculation, the flow–pressure ratio, flow efficiency, and inlet and outlet total temperatures and pressures align well with the experimental data. Furthermore, the resolution of the flow field structure related to the interaction between the tip leakage vortex and channel shock wave is high. (3) The turbulence model uses PAFV as the turbulence velocity scale, thereby suppressing the fluctuation velocity and turbulence viscosity near shock wave areas, preventing excessive turbulence viscosity. Moreover, PAFV inherently exhibits transport properties and anisotropic characteristics, making it well-suited for handling transonic compressor flows.