Abstract Sea surface temperature (SST) plays an important role in tropical cyclone (TC) life cycle evolution, but often the uncertainties in SST estimates are not considered in the ensemble Kalman filter (EnKF). The lack of uncertainties in SST generally results in the lack of ensemble spread in the atmospheric states near the sea surface, particularly for temperature and moisture. In this study, the uncertainties of SST are included by adding ensemble perturbations to the SST field, and the impact of the SST perturbations is investigated using the local ensemble transform Kalman filter (LETKF) with the Weather Research and Forecasting Model (WRF) in the case of Typhoon Sinlaku (2008). In addition to the experiment with the perturbed SST, another experiment with manually inflated ensemble perturbations near the sea surface is performed for comparison. The results indicate that the SST perturbations within EnKF generally improve analyses and their subsequent forecasts, although manually inflating the ensemble spread instead of perturbing SST does not help. Investigations of the ensemble-based forecast error covariance indicate larger scales for low-level temperature and moisture from the SST perturbations, although manual inflation of ensemble spread does not produce such structural effects on the forecast error covariance. This study suggests the importance of considering SST perturbations within ensemble-based data assimilation and promotes further studies with more sophisticated methods of perturbing SST fields such as using a fully coupled atmosphere–ocean model.