The joined-wing configuration SensorCraft, presents a more feasible way to meet tough design requirements such as long-endurance and 360-deg radar coverage compared to conventional and flying wing configurations. Proper assessment of the interactions between aerodynamics, structure, and embedded antenna in the optimization of the joined-wing SensorCraft is essential to obtain superior performances. This paper establishes the embedded radar performance estimation model and describes an integrated design process of aerodynamic, structure, and embedded radar performance of such an aircraft. Results show that multi-objective optimization leads to an increase of 14.76% in lift-to-drag ratio, 3.96% and 8.75% in the forward-looking and backward-looking radar detection ranges respectively. Moreover, the structural weight is reduced by 6.0% compared to that of the baseline design. Moreover, sensitivities of the rear wing dihedral angle, endplate height ratio, and joint location of the joined-wing configuration are analyzed in detail.