This research investigates the development of a robust control strategy for enhancing the 3D trajectory tracking performance of under-actuated lighter-than-air (LTA) systems in the presence of uncertainties and disturbances. Under-actuated LTA systems, characterized by limited control inputs relative to their degrees of freedom, pose significant challenges in achieving precise trajectory tracking, particularly when subjected to environmental disturbances and uncertainties in system parameters. To address this issue, we propose a novel approach that integrates a robust control strategy with uncertainty and disturbance estimation technique. The proposed methodology leverages a model-based controller designed to handle the under-actuated nature of LTA systems, ensuring stability and robustness in the presence of external disturbances. Additionally, a disturbance estimator is incorporated into the control loop to estimate and compensate for uncertainties in the system dynamics, enabling real-time adjustments to improve trajectory tracking accuracy. Simulation studies are conducted to validate effectiveness of the proposed approach and by comparing its performance with traditional control methods. Results demonstrate that the uncertainty and disturbance estimation-based strategy is effective in mitigating the impact of external perturbations and uncertainties on trajectory tracking accuracy.