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This paper presents a novel variational method for treating three-dimensional rotational Navier-Stokes equations in flow channel of turbomachines. The proposed method establishes a new semi-geodesic coordinate system on the central surface of blades. From the perspective of differential geometry, the system under concern is split into a set of membrane operator equations on two-dimensional manifolds and bending operator equations along hub circle. The third variable of the new coordinate system is approximated by the central difference scheme. We derive a new formulation of two-dimensional Navier-Stokes equations with three components on the manifolds in the variational sense. The well-posedness of the proposed variational formulation is rigorously justified. [ABSTRACT FROM AUTHOR]