Abstract Understanding how model physics impact tropical cyclone (TC) structure, motion, and evolution is critical for the development of TC forecast models. This study examines the impacts of microphysics and planetary boundary layer (PBL) physics on forecasts using the Hurricane Analysis and Forecast System (HAFS), which is newly operational in 2023. The “HAFS-B” version is specifically evaluated, and three sensitivity tests (for over 400 cases in 15 Atlantic TCs) are compared with retrospective HAFS-B runs. Sensitivity tests are generated by 1) changing the microphysics in HAFS-B from Thompson to GFDL, 2) turning off the TC-specific PBL modifications that have been implemented in operational HAFS-B, and 3) combining the PBL and microphysics modifications. The forecasts are compared through standard verification metrics, and also examination of composite structure. Verification results show that Thompson microphysics slightly degrades the days 3–4 forecast track in HAFS-B, but improves forecasts of long-term intensity. The TC-specific PBL changes lead to a reduction in a negative intensity bias and improvement in RI skill, but cause some degradation in prediction of 34-kt (1 kt ≈ 0.51 m s−1) wind radii. Composites illustrate slightly deeper vortices in runs with the Thompson microphysics, and stronger PBL inflow with the TC-specific PBL modifications. These combined results demonstrate the critical role of model physics in regulating TC structure and intensity, and point to the need to continue to develop improvements to HAFS physics. The study also shows that the combination of both PBL and microphysics modifications (which are both included in one of the two versions of HAFS in the first operational implementation) leads to the best overall results. Significance Statement A new hurricane model, the Hurricane Analysis and Forecast System (HAFS), is being introduced for operational prediction during the 2023 hurricane season. One of the most important parts of any forecast model are the “physics parameterizations,” or approximations of physical processes that govern things like turbulence, cloud formation, etc. In this study, we tested these approximations in one configuration of HAFS, HAFS-B. Specifically, we looked at two different versions of the microphysics (modeling the growth of water and ice in clouds) and boundary layer physics (the approximations for turbulence in the lowest level of the atmosphere). We found that both of these sets of model physics had important effects on the forecasts from HAFS. The microphysics had notable impacts on the track forecasts, and also changed the vertical depth of the model hurricanes. The boundary layer physics, including some of our changes based on observed hurricanes and turbulence-resolving models, helped the model better predict rapid intensification (periods where the wind speed increases quickly). Work is ongoing to improve the model physics for better forecasts of rapid intensification and overall storm structure, including storm size. The study also shows the combination of both PBL and microphysics modifications overall leads to the best results and thus was used as one of the two first operational implementations of HAFS.