Turbomachinery blade rows can have non-uniform geometries due to design intent, manufacture errors or wear. When predictions are sought for the effect of such non-uniformities, it is generally the case that whole assembly calculations are needed. A spectral method is used in this paper to approximate the flow fields of the whole assembly but with significantly less computation cost. The method projects the flow perturbations due to the geometry non-uniformity in an assembly in Fourier space, and only one passage is required to compute the flow perturbations corresponding to a certain wave-number of geometry variation. The performance of this method on transonic blade rows is demonstrated on a modern fan assembly. Low engine order and high engine order geometry non-uniformity (e.g., “saw-tooth” pattern) are examined. The non-linear coupling between the flow perturbations and the passage-averaged flow field is also demonstrated. Pressure variations on the blade surface and the potential flow field upstream of the leading edge from the proposed spectral method and the direct whole assembly solutions are compared. Good agreement is observed on both quasi-3D and full 3D cases. A lumped approach to compute deterministic fluxes is also proposed to further reduce the computational cost of the spectral method. The spectral method is formulated in such a way that it can be easily implemented into an existing harmonic flow solver by adding an extra source term and can be potentially used as an efficient tool for aeromechanical and aeroacoustics design of turbomachinery blade rows.