In order to enhance the wind-resistance capability and achieve a lightweight design of high-altitude unmanned airships, this study proposes a rapid optimization method for a heterogeneous propeller propulsion system. This system integrates contra-rotating and ducted propellers to exploit their respective aerodynamic advantages. First, surrogate models of the contra-rotating propeller, contra-rotating motor, ducted propeller, and ducted motor were constructed using an optimal Latin hypercube sampling method based on the max–min criterion. Then, within the optimization framework, propeller–motor matching principles and energy balance constraints were incorporated to minimize the total weight of the propulsion and energy systems. A case study on a conventional high-altitude unmanned airship demonstrates that, under the same wind-resistance capability, the adoption of the heterogeneous propeller electric propulsion system reduces the total propulsion-and-energy system weight by 24.94%. This method integrates the advantages of contra-rotating and ducted propellers, thereby overcoming the limitations of conventional propulsion architectures. It provides a new approach for designing lightweight, efficient, and long-endurance propulsion systems for near-space high-altitude platforms.