To address the issues of complex structure, excessive weight, CT artifacts, and redundant degrees of freedom in six-degree-of-freedom external fixators during bone treatment, a configuration optimization approach for parallel external fixators was proposed to meet differentiated therapeutic requirements. Based on a modular design concept, the system was decomposed into ring modules and connecting modules, with definitions established for module types, assembly protocols, and connection rules. Utilizing optimization algorithms, a digital configuration scheme for parallel external fixators was developed, transforming three-dimensional models into two-dimensional representations. By integrating feasibility requirements and optimization objectives, a "rigid-flexible coupling" constraint framework was formulated for the fixator configuration. For varied clinical demands, the performance of two multi-objective optimization algorithms was compared, and the more robust algorithm was selected as the configuration optimization method. Finally, through combined validation using physical prototypes and simulation models, the optimized configuration demonstrated effectiveness in resolving targeted clinical challenges while maintaining structural stability, thereby verifying the proposed optimization methodology.