Abstract: To address the challenges of compact size and tracking accuracy in Unmanned Aerial Vehicle (UAV) electro-optical (EO) pods, this study proposes a co-optimization approach that integrates non-orthogonal structural design with advanced control algorithms. A 45°-tilted non-orthogonal three-axis pod model was established, and kinematic analysis revealed decoupled dynamics between gyroscopic sensors and motors. Comparative evaluations of three tracking controllers—proportional-integral (PI), sliding mode, and YouLa parameterized—demonstrated the superior performance of the YouLa controller, achieving a 65° phase lead and a 50% reduction in off-target amplitude under 0.5 Hz sinusoidal perturbations. The non-orthogonal architecture reduces the horizontal footprint by 30% while maintaining precision and effectively addressing UAV payload constraints. This structural-control synergy enables rapid and accurate tracking of slow-moving small targets, offering a novel paradigm for lightweight EO pod development with potential scalability to multitarget scenarios.