Sampling error stems from the use of ensemble-based data assimilation (EDA) with a limited ensemble size and can result in spurious background error covariances, leading to false analysis corrections. The WRF-LETKF radar assimilation system (WLRAS) is performed separately with 256 and 40 members to investigate the characteristics of convective-scale sampling errors in the EDA and its impact on precipitation prediction based on a heavy rainfall event on 16 June 2008. The results suggest that the sampling errors for this event are sensitive to the relationships between the simulated observations and model variables, the intensity of reflectivity, and how the prevailing wind projects to the radial wind in the areas that the radar cannot resolve U or V wind. The sampling errors lead to an underprediction of heavy rainfall when the horizontal localization radius is inadequately large, but this can be mitigated when a more accurate moisture condition is provided. In addition, being able to use a larger vertical localization plays an important role in providing necessary adjustments for representing the vertical thermodynamical structure of convection, which further improves precipitation prediction. A strategy mitigating the impact of sampling errors associated with the limitation of radial wind measurement by inflating the observation error over sensitive areas can bring benefits to precipitation prediction.