The invention discloses a multi-harmonic multi-input multi-output feedforward self-adaptive controlling method for helicopter body vibration and belongs to the field of active controlling of helicopter vibration. Aiming at the characteristic of helicopter body vibration under stimulation of the rotor vibration load with multi-stage harmonic frequency and multiple directions and based on the minimum mean square error method and harmonic coefficient identification, the multi-input multi-output feedforward self-adaptive controlling method of helicopter body vibration under the multi-harmonic and multi-load simulation is put forward, so that the purpose of reducing helicopter body vibration is achieved, and when the vibration phase, vibration amplitude and vibration frequency are changed, the good self-adaptive controlling performance is achieved.