Procambarus clarkia is one of the species of crayfish. It is often required for the accurate discrete element method (DEM) bonding parameters and empirical data in the head–tail separation of the Procambarus clarkii. The mechanical processing equipment can also be optimized during this time. Taking the Procambarus clarkii as the research subject, this study aims to calibrate and optimize the parameters in the double-layer flexible discrete element bonding model. The significant disparity was considered in the material hardness between the exoskeletal shell and internal muscle tissue. A dual-layer flexible DEM bonding model was developed after consideration. According to the Bonding V2 framework, a regular and densely packed shell mesh was generated using a coordinate Meta-Particle packing approach. The crayfish shell was obtained as the structured representation. In parallel, the internal muscle tissue was modeled using a volume-packing strategy in order to simulate the heterogeneous mixture of muscle fibers and interstitial fluids. The separate calibration of bonding parameters was obtained for the shell and muscle components, which were subsequently integrated into a composite whole-body crayfish model. The resulting dual-layer structure effectively captured the distinct mechanical features of the shell. A solid foundation was offered for the accurate simulation of the head–tail separation. Mechanical tests were conducted using a texture analyzer in order to obtain the empirical reference values. These values served as the benchmarks for the simulation validation and parameter optimization. A series of simulation experiments was conducted, including the single-factor tests, two-level factorial analysis tests, and the steepest ascent tests. The maximum shearing force was taken as the primary evaluation index. Pareto charts and analysis of variance (AVONA) were adopted to identify the significant factors among the bonding parameters and their effective ranges. As such, the response surface method (RSM) was applied to determine the optimal combination of significant factors for the crayfish shell and muscle tissue bonding. The optimal dataset of the bonding parameter was determined as follows: the normal stiffness per unit area of the crayfish shell was 2.19 × 10¹¹ $\mathrm{N}/{\mathrm{m}}^3$, the critical normal strength of the shell was 6.04 × 10⁶ Pa, and the critical normal strength of the muscle tissue was 7.77 × 10⁷ Pa. These parameters were then implemented in the EDEM simulation software. The virtual tests were carried out to replicate the head-tail cutting and breaking processes. The results show that the simulation closely matched the experimental measurements. These tests involved both shearing and breaking separation trials on the crayfish head-tail region. The maximum shearing force was recorded as 31.97 N, while the maximum breaking force was 26.39 N. The relative error for the maximum cutting force was only 0.22%, and for the maximum breaking force, it was 3.87%. Furthermore, the overall trend in the force variation was consistent with that in the physical tests. These findings demonstrate that the DEM bonding parameters were calibrated to be highly reliable for the mechanical separation behavior of the Procambarus clarkii. In conclusion, this finding can provide a robust performance to simulate the head-tail separation in red swamp crayfish using discrete element modeling. The findings can greatly contribute to the valuable theoretical foundation for the design and optimization of the mechanical equipment in aquatic product processing, particularly for the automation and efficiency improvements in crayfish disassembly systems.