The current demand for aircraft panel assembly fixtures necessitates agile manufacturing solutions. Traditional welding fixtures struggle to meet diverse panel types, high quantities, and short manufacturing cycles. Conversely, reconfigurable flexible assembly fixtures offer universality, efficiency and ease of maintenance but heavily rely on designers' experience, hindering knowledge reuse. Existing research on computer-aided fixture design (CAFD) primarily addresses specialized fixtures, neglecting reconfigurable flexible ones, lacking fixture design knowledge systems. Aiming at the above problems, the study proposes an intelligent design method for the reconfigurable flexible assembly fixture for aircraft panels based on the smart composite jig model (SCJM) and knowledge graph (KG). Firstly, based on the SCJM of the aircraft panel type assembly fixture (PSCJM), a configuration design method is proposed to carry out the multi-level design of reconfigurable assembly fixture to instantiate PSCJM containing fixture configuration rules and a module library based on model definition (MBD). Then, a knowledge retrieval method is proposed to search the suitable fixture design knowledge based on KG, assisting designers in achieving the flexible design of aircraft panel reconfigurable assembly fixtures. Finally, practical engineering design validation confirms the method's feasibility and effectiveness in obtaining the reconfigurable flexible assembly fixture design scheme for aircraft panels.