Estimating the structural weight of a Hybrid Wing Body (HWB) aircraft during conceptual design has proven to be a significant challenge due to its unconventional configuration. Aircraft structural weight estimation is critical during the early phases of design because inaccurate estimations could result in costly design changes or jeopardize the mission requirements and thus degrade the concept's overall viability. The tools and methods typically employed for this task are inadequate since they are derived from historical data generated by decades of tube-and-wing style construction. In addition to the limited applicability of these empirical models, the conceptual design phase requires that any new tools and methods be flexible enough to enable design space exploration without consuming a significant amount of time and computational resources. This thesis addresses these challenges by developing a parametric and physics-based modeling and simulation (M&S) environment for the purpose of HWB structural weight estimation. The tools in the M&S environment are selected based on their ability to represent the unique HWB geometry and model the physical phenomena present in the centerbody section. The new M&S environment is used to identify key design parameters that significantly contribute to the variability of the HWB centerbody structural weight and also used to generate surrogate models. These surrogate models can augment traditional aircraft sizing routines and provide improved structural weight estimations.