A frequency-tunable resonance scattering lidar with high temporal/vertical resolutions (1 min/15 m) observed sporadic calcium ion (Ca-s(+)) layers at similar to 100 km over Tachikawa (geographical/geomagnetic latitude: 35.7 degrees N/27.1 degrees N), Japan, on 21-22 August 2014. Simultaneously, sporadic E (E-s) parameters and medium-scale traveling ionospheric disturbances (MSTIDs) were observed by an ionosonde and Global Navigation Satellite System receiver network, GEONET, respectively. The maximum densities of the Ca+ and electrons in the E-s layer had a strong positive correlation. As observation started similar to 23:30 LT, the Ca-s(+) layer and the associated E-s layer descended at similar to 2.8 km/hr with density irregularities including Kelvin-Helmholtz billow-like structures suggesting the presence of background neutral wind shear and instability. And the total electron content variations showed large amplitude associated with the MSTIDs at an altitude of 300 km in synchronization with the Ca+ column abundance surges at 100 km over Tachikawa; in their respective E and F region locations connected by geomagnetic field line these irregularities are found to vary in phase. At similar to 02:00 LT, the Ca-s(+) layer stopped descending at similar to 100 km due to larger ion-neutral collision frequency in the lower altitudes and resided there quietly until sunrise; both Ca+ column abundance enhancements and the large total electron content variation disappeared as the descent of the Ca-s(+) layer stopped, implicating that the MSTID structure cannot be sustained without the density irregularities of the E-s layer. This is the first synchronous observation of the coupling between the E-s density irregularities and the MSTIDs in the F region along a common magnetic flux tube.Plain Language Summary The irregular structures of the sporadic E (E-s) layer appearing in altitudes of 90-130 km were observed by a calcium ion (Ca+) resonance scattering lidar and an ionosonde. Simultaneously, medium-scale traveling ionospheric disturbances (MSTIDs) in the F region (150- to 500-km altitude) were observed by the Global Navigation Satellite System receiver array in Japan. Though the electron column abundance variation in the E-s irregularities is more than an order of magnitude smaller than that in the MSTIDs, we observed that the MSTIDs decayed with the disappearance of the irregular structure in the E-s layer. This observation clearly revealed for the first time that the plasma density irregularities in the E region were coupled to those in the F region by the geomagnetic field line as theory predicted.