Abstract This study investigated variations in the Madden–Julian oscillation (MJO) behavior between two types of La Niña winters: mega and equatorial La Niñas. Results of this work show that in contrast to mega conditions, accompanied by more abundant intraseasonal column-integrated moisture anomalies over the planetary boundary layer, intensities of intraseasonal outgoing longwave radiation anomalies are stronger over the tropical western Pacific (WP) at MJO phases 5–6 under equatorial conditions. The occurrence of the moisture anomaly change averaged over the tropical WP is supported by a distinct moisture tendency difference. Moisture budget and multiscale interaction diagnoses underscore the pivotal effect of an area-averaged vertical gradient change in low-frequency background moisture in driving such tendency change. Considering notable MJO convection variations, the teleconnections associated with MJO phases 5–6 over East Asia (EA) were also explored, including warmer surface air temperature anomalies and stronger positive geopotential height anomalies at 200 hPa on the intraseasonal time scale under equatorial conditions. Results from a linear baroclinic model demonstrate that such teleconnection changes could be effectively explained by the linear response to the MJO’s diabatic heating anomaly. Roles of mean state and MJO itself variations in the linear response change are also discussed. These findings provide novel insights into MJO activity and offer potential improvements for subseasonal forecasting in EA. Significance Statement The relationship between El Niño–Southern Oscillation (ENSO) and MJO has been extensively explored recently. However, variations in the MJO behavior and its climate effects under mega and equatorial La Niña winters have not been thoroughly investigated. In this work, we utilized reanalysis datasets and an idealized linear baroclinic model to address these questions. We observed more robust and abundant intraseasonal convection activity and planetary boundary layer–integrated moisture anomaly averaged over the tropical WP at MJO phases 5–6 under equatorial conditions than mega conditions, which is closely linked with the vertical gradient change in low-frequency background moisture. Additionally, MJO-related teleconnections also exhibit some changes. This work may provide a new perspective on understanding the relationship between the MJO and ENSO and offer potential improvements for the subseasonal forecast.