This paper presents a novel trajectory tracker for autonomous quadrotor navigation in dynamic and complex environments. The proposed framework integrates a distributional Reinforcement Learning (RL) estimator for unknown aerodynamic effects into a Stochastic Model Predictive Controller (SMPC) for trajectory tracking. Aerodynamic effects derived from drag forces and moment variations are difficult to model directly and accurately. Most current quadrotor tracking systems therefore treat them as simple ‘disturbances’ in conventional control approaches. We propose Quantile-approximation-based Distributional Reinforced-disturbance-estimator, an aerodynamic disturbance estimator, to accurately identify disturbances, i.e., uncertainties between the true and estimated values of aerodynamic effects. Simplified Affine Disturbance Feedback is employed for control parameterization to guarantee convexity, which we then integrate with a SMPC to achieve sufficient and non-conservative control signals. We demonstrate our system to improve the cumulative tracking errors by at least 66% with unknown and diverse aerodynamic forces compared with recent state-of-the-art. Concerning traditional Reinforcement Learning’s non-interpretability, we provide convergence and stability guarantees of Distributional RL and SMPC, respectively, with non-zero mean disturbances.