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Abstract The 12‐year continuous observation of gravity wave momentum fluxes (GWMFs) estimated by the Mohe meteor radar (53.5°N, 122.3°E) revealed prominent intraseasonal variability around the extratropical mesopause (82–94 km) during boreal winters. Composite analysis of the December‒January‒February (DJF) season according to the Madden‒Julian Oscillation (MJO) phases revealed that the zonal GWMFs notably increased in MJO Phase 4 (P4) by ∼2–4 m²/s², and a Monte Carlo test was designed to examine the statistical significance. The response in zonal winds lags behind the GWMF response by two MJO phases (i.e., 1/2π), indicating a “force‒response” interaction between them. Additionally, time‐lagged composites revealed that strengthened westward GWMFs occurred ∼25–35 days after MJO P4, coincident with the MJO impact on the zonal winds in the stratosphere. The analysis results also suggested that the mechanism of MJO by which the MJO influences the stratospheric circulation might involve poleward propagating effects of stationary planetary waves with zonal wavenumber one. This work emphasizes the importance of GW intraseasonal variability, which impacts tropical sources from the troposphere to the extratropical mesopause.