Abstract An initial vortex spindown, or strong adjustment to the structure and intensity of a hurricane’s initial vortex, presents a significant problem in hurricane forecasting, as with the NCEP Hurricane Weather Research and Forecasting Model (HWRF), because it can cause significantly degraded intensity forecasts. In this study, the influence of the self-consistent regional ensemble background error covariance on assimilating hurricane inner-core tail Doppler radar (TDR) observations in HWRF is examined with the NCEP gridpoint statistical interpolation (GSI)-based ensemble–three-dimensional variational (3DVAR) hybrid data assimilation system. It is found that the resolution of the background error covariance term, coming from the ensemble forecasts, has notable influence on the assimilation of hurricane inner-core observations and subsequent forecasting results. Specifically, the use of ensemble forecasting at high-resolution native grids results in significant reduction of the vortex spindown problem and thus leads to improved hurricane intensity forecasting. Further diagnoses are conducted to examine the spindown problem with a gradient wind balance. It is found that artificial vortex initialization, performed before data assimilation, can cause strong supergradient winds or imbalance in the vortex inner-core region. Assimilation of hurricane inner-core TDR data can significantly mitigate this imbalance by reducing the supergradient effects. Compared with the use of a global ensemble background error term, application of the self-consistent regional ensemble background covariance to inner-core data assimilation leads to better representation of the mesoscale hurricane inner-core structures. It can also result in more realistic vortex structures in data assimilation even when the observational data are unevenly distributed.