A three-dimensional aerodynamic shape optimization technique in inviscid compressible flows is developed by using a parallel continuous adjoint formulation on unstructured meshes. A new surface mesh modification method is proposed to overcome difficulties related to patch-level remeshing for unstructured meshes, and the effect of design sections on aerodynamic shape optimization is examined. Applications are made to three-dimensional wave drag minimization problems including an ONERA M6 wing and the EGLIN wing-pylon-store configuration. The results show that the present method is robust and highly efficient for the shape optimization of aerodynamic configurations, independent of the number of design variables used.