The mesopause, a boundary between mesosphere and thermosphere with the coldest atmospheric temperature, is formed mainly by the combining effects of radiative cooling of CO2, and the vertical adiabatic flow in the upper atmosphere. A continuous multidecade (1990‐2018) nocturnal temperature data base of an advanced Na lidar, obtained at Fort Collins, CO (41°N, 105°W), and at Logan, UT (42°N, 112°W), provides an unprecedented opportunity to study the long‐term variations of this important atmospheric boundary. In this study, we categorize the lidar‐observed mesopause into two categories: the “high mesopause” (HM) above 97 km during nonsummer months, mainly formed through the radiative cooling, and the “low mesopause” (LM) below 92 km during nonwinter months, generated mostly by the adiabatic cooling. These lidar observations reveal a cooling trend of more than 2 K/decade in absolute mesopause temperature since 1990, along with a decreasing trend in mesopause height: The HM is moving downward at a speed of ~ 450 ± 90 m/decade, while the LM has a slower downward trend of ~ 130 ± 160 m/decade. However, since 2000, while the height trend (‐ 470 ± 160 m/decade for the HM and 150 ± 290 m/decade for the LM) is consistent, the temperature trend becomes statistically insignificant (‐ 0.2 ± 0.7 K/decade and ‐1 ± 0.9 K/decade for the HM and the LM, respectively). A long‐term study by Whole Atmosphere Community Climate Model with thermosphere and ionosphere extension (WACCM‐X) also indicated the similar mesopause changes, mostly caused by stratosphere‐lower mesosphere cooling and contraction.