Based on the shape and performance characteristics of the wing-body fusion layout UAV, a multidisciplinary comprehensive analysis model, comprehensive evaluation model and optimization model suitable for the overall scheme of the UAV in the conceptual design stage are established, and the corresponding tools are developed. The geometric, weight, aerodynamic and stealth characteristics of the overall scheme of the wing-body fusion layout UAV are analyzed by combining numerical analysis and engineering methods. The improved TOPSIS method is used to establish a comprehensive evaluation model from the perspective of the loading capacity, economy and adaptability of the UAV. The rationality of the analysis model is verified by taking multiple UAV schemes as examples. Using the parallel subset simulation optimization algorithm, the traditional multi-objective optimization is completed with the maximum cruise lift-to-drag ratio and the minimum forward RCS as the goal, and the scheme optimization based on comprehensive evaluation is completed with the strongest competitiveness as the goal. Based on all the schemes generated by the multi-objective optimization process, the parameter correlation analysis is completed, and the influence of the span, sweep angle and twist angle on the aerodynamic and stealth characteristics is verified. The RCS of the final multi-objective optimization scheme is reduced 41.6%, and the cruise lift-to-drag ratio is improved 3.5% ; the competitiveness score of the comprehensive evaluation optimization scheme is improved 44.0%.