This study focuses on the poorly known effect of polar cap patches (PCPs) on the ion-neutral coupling in the F-region. The PCPs were identified by total electron content measurements from the Global Navigation Satellite System (GNSS) and the ionospheric parameters from the Defense Meteorological Satellite Program spacecraft. The EISCAT incoherent scatter radars on Svalbard and at Troms & oslash;, Norway observed that PCPs entered the nightside auroral oval from the polar cap and became plasma blobs. The ionospheric convection further transported the plasma blobs to the duskside. Simultaneously, long-lasting strong upper thermospheric winds were detected in the duskside auroral oval by a Fabry-Perot Interferometer (FPI) at Troms & oslash; and in the polar cap by the Gravity Recovery and Climate Experiment satellite. Using EISCAT ion velocities and plasma parameters as well as FPI winds, the ion drag acting on neutrals and the time constant for the ion drag could be estimated. Due to the arrival of PCPs/blobs and the accompanied increase in the F-region electron densities, the ion drag is enhanced between about 220 and 500 km altitudes. At the F peak altitudes near 300 km, the median ion drag acceleration affecting neutrals more than doubled and the associated median e-folding time decreased from 4.4 to 2 hr. The strong neutral wind was found to be driven primarily by the ion drag force due to large-scale ionospheric convection. Our results provide a new insight into ionosphere-thermosphere coupling in the presence of PCPs/blobs. This study investigates how the evolution of the polar cap patches (PCPs) affects the upper layer of the Earth's atmosphere, termed the thermosphere. PCPs are dense patches of charged particles that move from the dayside to the nightside of the high-latitude ionosphere through the polar cap region. Using the measurements by multiple ground-based instruments and satellites, this study found that PCPs can enhance the formation of strong upper thermospheric winds. The winds are primarily driven by the ion drag force due to the interactions between charged particles and neutral gases. The results show that because of the arrival of PCPs, which increase the F-region electron densities in the auroral oval, the ion drag acceleration acting on the neutrals can more than double and the related time constant of the ion drag can be halved. Transportation of polar cap patches (PCPs) and their development in the nightside auroral oval was observed by multiple instruments Very strong, long-lasting westward upper thermospheric wind in the duskside oval was associated with large-scale ionospheric convection High electron density produced by PCPs increases the ion drag force that drives the upper thermospheric wind