Isogeometric analysis(IGA) is applied to eigenvalue problem of waveguide with arbitrary cross-section.Weakened equations are involved with NURBS elements from governing equation of waveguide.The computational model in IGA is inherited from a design model in CAD system,which is beyond traditional numerical method with remodeling procedure.Elliptical waveguides with various eccentricities,triangular and pentagon waveguides are addressed as numerical examples.It demonstrates that the preseut method is feasible for eigenvalue analysis of waveguide with either elliptical or polygonal cross-section.Moreover,it yields excellent results with fewer DOFs,and obtains quicker convergence than traditional method.