We present a multi-instrument experiment to study the effects of tropospheric thunderstorms on the mesopause region and the lower ionosphere. Sodium (Na) lidar and ionospheric observations by two digital ionospheric sounders are used to study the variation in the neutral metal atoms and metallic ions above thunderstorms. An enhanced ionospheric sporadic E layer with a downward tidal phase is observed followed by a subsequent intensification of neutral Na number density with an increase of 600 cm−3 in the mesosphere. In addition, the Na neutral chemistry and ion-molecule chemistry are considered in a Na chemistry model to simulate the dynamical and chemical coupling processes in the mesosphere and ionosphere above thunderstorms. The enhanced Na layer in the simulation obtained by using the ionospheric observation as input is in agreement with the Na lidar observation. We find that the intensification of metallic layered phenomena above thunderstorms is associated with the atmospheric tides, as a result of the troposphere-mesosphere-ionosphere coupling.