In this paper, we consider an optimal control problem governed by Stokes equations with $H^1$-norm state constraint. The control problem is approximated by spectral method, which provides very accurate approximation with a relatively small number of unknowns. Choosing appropriate basis functions leads to discrete system with sparse matrices. We first present the optimality conditions of the exact and the discrete optimal control systems, then derive both a priori and a posteriori error estimates. Finally, an illustrative numerical experiment indicates that the proposed method is competitive, and the estimator can indicate the errors very well.