Magnetic levitation has been applied to maglev trains and magnetic suspension wind tunnel. However, there are some problems with the existing levitation control. For example, it is difficult to extract smooth velocity signals from the gap sensor with noise. The classical differentiator is susceptible to noise, which makes the levitation system sometimes vibrate. The accuracy and stability of levitation control need to be improved. The velocity fusion estimation method (VFE) is proposed to extract the velocity signal from the gap and acceleration sensor, which is theoretically derived to prove that it reduced the noise of the velocity signal. Then disturbance rejection control(DRC) is proposed that add VFE into classical levitation control. Because of the high-quality velocity signal and accelerometer's fast responsiveness, it makes DRC have many advantages. The advantages of using the proposed control structure are that it improved the control accuracy of the target gap and resisted disturbance effectively. Air-gap fluctuations in levitation systems can be reduced in transient pulse disturbance test, white noise disturbance test, and external force disturbance test when it applies the proposed control method. The effectiveness and advantages of the proposed control method are verified by the simulation and experiments.