Blended-Wing-Body (BWB) aircraft is promoted as one of the most possible layouts to achieve more sustainable civil aviation. Due to the non-circular cross-section of the center-body, a bulge deformation forms over the upper surface of the body under the coupled loads of the internal pressurization of the cabin and the aerodynamic bending moments of the wing, which reduces the lift-to-drag ratio of BWB aircraft. Under a limited deformation, the relationship between the aerodynamic performance and the structural weight needs to be studied. In this work, the effects of stiffness constraints on the center-body deformation, structural weight of the airframe and aerodynamic performance were investigated by using an analytical model of the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) for the airframe and the computational fluid dynamics method, respectively. The results show that as the stiffness constraint increases, the spacings between the rod stringers and the frame stiffeners decrease, and the structural weight increases inversely. A 5.2% reduction of the lift-to-drag ratio is encountered at cruise for a medium deformation design of 42.8 mm/m. A higher aerodynamic penalty is suffered when the stiffness constraint is further released. The final deformation criterion is different when the weight vector of the aerodynamic performance and structural weight is different.