In this work, we study shape optimization problems in the Stokes flows. By phase-field approaches, the resulted total objective function consists of the dissipation energy of the fluids and the Ginzburg–Landau energy functional as a regularizing term for the generated diffusive interface, together with a Lagrangian multiplier for volume constraint. An efficient decoupled scheme is proposed to implement by the gradient flow approach to decrease the objective function. In each loop, we first update the velocity field by solving the Stokes equation with the phase field variable given in the previous iteration, which is followed by updating the phase field variable by solving an Allen–Cahn-type equation using a stabilized scheme. We then take the cut-off post-processing for the phase-field variable to constrain its value in [0,1]. In the last step of each loop, the Lagrangian parameter is updated with an appropriate artificial time step. We rigorously prove that the proposed scheme permits an unconditionally monotonic-decreasing property. To enhance the overall efficiency of the algorithm, in each loop we update the phase field variable and Lagrangian parameter several time steps but update the velocity field only one time. Numerical results for various shape optimizations are presented to validate the effectiveness of our numerical scheme.