According to the automobile industry's flexible manufacturing requirements, a novel flexible fixturing system for sheet metal assembly is proposed with parallel robots. A methodology of the structure synthesis is presented by taking account simultaneously several performance indices. Taking the 3UPU/UPS parallel robot in the system as an example, models of inverse kinematics, Jacobian matrix and design space are developed. Thus, the structure synthesis of the parallel robot is simplified to a two-dimensional problem. Once the performance indices (workspace, singularity and stiffness) are established, the corresponding indices atlases are expressed in the design space. The structure parameters of the parallel robot are obtained by analyzing these atlases. The prototype of the fixturing system is developed, and the relevant clamping and stiffness experiments are conducted. The experimental results generally agree well with the simulation results and satisfy the flexible fixturing systems' requirements.