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A zonal decoupling algorithm used to control a dual deformable mirror (DM) is proposed. One of the two DMs is characterized with a large stroke (woofer), while the other one is characterized by a high spatial frequency (tweeter). A numerical model is used to compare the zonal decoupling algorithm with some traditional zonal decoupling algorithms. The simulation results indicate that the algorithm presented in this Letter improves the performance in suppressing the coupling error. An experimental system is built to prove the effectiveness of this algorithm. The experiments demonstrate that the phase aberrations could be effectively compensated and that the coupling error could also be suppressed.