A method of controlling a mechanical ventilator is provided which is capable of increasing a stability margin in the controlling of a gas-delivery mechanism for the mechanical ventilator. The flow rate F of an assisting gas is measured, and an observer 54 estimates a flow rate {circumflex over (F)} of the assisting gas. A difference ΔF between the measured flow rate F and estimated flow rate {circumflex over (F)} is then determined, and information on a patient's respiratory effort pressure Pmus is obtained. A target pressure Pin for controlling a gas-delivery mechanism 20 is calculated on the basis of this information. When the target pressure Pin is calculated on the basis of the flow-rate difference ΔF, an allowance with respect to the stability limit of the overall system 14 can be increased. This enables the runaway to rarely occur even when an actual overall system is varied. Moreover, the responsibility of assist respiration can be improved as compared with that of the related art PAV method.