We introduce an adaptive finite element method for computing electromagnetic guided waves in a closed, inhomogeneous, pillared three-dimensional waveguide at a given frequency based on the inverse iteration method. The problem is formulated as a generalized eigenvalue problems. By modifying the exact inverse iteration algorithm for the eigenvalue problem, we design a new adaptive inverse iteration finite element algorithm. Adaptive finite element methods based on a posteriori error estimate are known to be successful in resolving singularities of eigenfunctions which deteriorate the finite element convergence.We construct a posteriori error estimator for the electromagnetic guided waves problem.Numerical results are reported to illustrate the quasi-optimal performance of our adaptive inverse iteration finite element method.