In order to stabilize the engineering ships under low speed and improve its seakeeping at anchor and low speed, the control strategy of a fin stabilizer at low speed is proposed. Two main problems, such as the phase between the fin angle and the lift is very sensitive at low speed and the ship roll model has uncertainty, are studied. A numerical iterative method is introduced to solve the phase sensitivity at low speed and the nonlinear relationship between the lift and the fin angle. The phase adjuster can overcome the influence of speed measurement error to ensure the best phase matching. A fractional order robust controller is used to ensure the control performance of the fin stabilizer system when the model parameters are varying. A numerically simulate of the proposed control strategy is done, and the simulation data show that under the random ocean environment disturbance, the fin stabilizer can obtain satisfactory stabilizing effect under low speed. Finally, ship model testes in towing tank are carried out, and the test results also show that the designed control strategy can provide satisfactory anti-rolling effect at anchor and low speed.