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A desingularized high order panel method based on Non-Uniform Rational B-Spline (NURBS) was developed to deal with three-dimensional potential flow problems. A NURBS surface was used to precisely represent the body geometry. Velocity potential on the body surface was described by the B-spline after the source density distribution on the body surface had been solved. The collocation approach was employed to satisfy the Neumann boundary condition and Gaussian quadrature points were chosen as both the collocation points and the source points. The singularity was removed by a combined method, so the process of the numerical computation was non-singular. In order to verify the method proposed, the unbounded flow problems of sphere and ellipsoid, the wave-making problem of a submerged ellipsoid were chosen as computational examples. It is shown that the numerical results are in good agreement with analytical solutions and other numerical results in all cases, and sufficient accuracy of numerical solution can be reached with a small number of panels.