Structural flexibility of large transport results unavoidable coupling between control system and structural dynamics due to the application of large amounts of light material. Control system design for such aircraft should consider contribution from structural flexibility, and satisfy the specifications from flying qualities. To consider elastic modes in aircraft control system synthesis process, a novel H∞ loop shaping design procedure was given. Inner loop feedback gain was calculated by rigid flight dynamic model to satisfy specifications from flying qualities requirements and atmospheric turbulence rejection. The initial static output feedback gain obtained by rigid truncated model was used as weight for the high order model. Dynamic controller was consequently given by Glover-McFarlane-s H∞ loop shaping method to keep system stable while elastic modes are involved in the high order model. A typical numerical model and simulation in time domain were given to compare with the original design and better response shape and elastic modes suppression were shown.