To improve the flowrate control accuracy of fuel control system at high supply pressure and large flowrate working condition, this paper proposes a novel dual closed-loop control for fuel metering unit (FMU) to address issues related to unknown velocity, matched/unmatched disturbances, and parameter uncertainties. Firstly, for a comprehensive assessment in flowrate feedback method, a global sensitive analysis is utilized to research the effect ratio of factors affecting the discharge flowrate. Then, a novel dual closed-loop control is proposed, in which the outer loop is flowrate loop, and a novel extended-state-observer (ESO)-based robust adaptive control without velocity sensor is used as the internal displacement loop control. Specifically, ESO can effectively estimate the unknown velocity and unmatched disturbance, and the parameter estimations can be updated by the adaptive law determined only by spool displacement and reference signal. The novel robust control can address matched/unmatched disturbances and model uncertainties effectively. Through Lyapunov method, it follows that the novel ESO-based robust adaptive control can achieve asymptotic tracking performance when occurring time-invariant disturbances and bounded tracking performance when occurring time-varying disturbances. Comparative experiments verify the superiority of the proposed control, which provides a new method and glimpse for the advanced control strategy of aeroengine.