This study introduces a novel methodology for controlling Quadrotor Unmanned Aerial Vehicles, focusing on Hierarchical Sliding Mode Control strategies and an Extended Kalman Filter. Initially, an EKF is proposed to enhance robustness in estimating UAV states, thereby reducing the impact of measured noises and external disturbances. By locally linearizing UAV systems, the EKF can mitigate the disadvantages of the Kalman filter and reduce the computational cost of other nonlinear observers. Subsequently, in comparison to other related work in terms of stability and computational cost, the HSMC framework shows its outperformance in allowing the quadrotor UAVs to track the references. Three types of HSMC Aggregated HSMC, Incremental HSMC, and Combining HSMC are investigated for their effectiveness in tracking reference trajectories. Moreover, the stability of the quadrotor UAVs is rigorously analyzed using the Lyapunov stability principle. Finally, experimental results and comparative analyses demonstrate the efficacy and feasibility of the proposed methodologies.