When quadrotor unmanned aerial vehicles (UAVs) operate in urban low-altitude airspace, especially within complex environments, their sensor perception signals are highly susceptible to blockages, deviations, and the inclusion of high-frequency noise. These factors, in turn, induce nonlinear variations in the UAVs’ flight mechanical properties, giving rise to abnormal flight stability issues such as attitude jitter, altitude fluctuations, and trajectory deviations. To address these challenges, this paper puts forward a method aimed at enhancing the positional accuracy of quadrotor UAVs, which is based on Extended Kalman Filter (EKF) multi-sensor fusion. In conjunction with the redundant configuration of sensors, a proportional-integral controller is specifically designed to allow optical flow sensors to compensate for the speed data generated by inertial sensors. Building on the EKF method, a comprehensive data fusion model is established, encompassing both position and speed states. Leveraging the MATLAB platform, trajectory flight simulations are conducted, utilizing multi-sensor data fused via EKF, with the sensor suite including GPS, IMU, Optical Flow sensors, and Barometers. The simulation results demonstrate that this proposed method can effectively mitigate the adverse impacts of environmental interference and sensor noise on the positional accuracy of quadrotors. By continuously correcting position information and accurately estimating position states, it significantly improves the UAVs’ flight position accuracy. This research outcome lays a robust and theoretically sound foundation for in-depth investigations on critical issues related to general aviation applications, such as the safe and efficient autonomous flight, adaptive and reliable intelligent navigation, and ultra-precise and mission-critical operations of quadrotor UAVs, thereby significantly contributing to the sustained and innovative advancement of the field.