The Maritime Continent rainfall typically shows negative anomalies during El Niño. However, during boreal winter, the rainfall response to El Niño is spatially heterogeneous, with a few areas experiencing positive anomalies. This study investigates whether the wintertime ENSO-rainfall relationship is stationary or has undergone long-term modulation using multiple precipitation datasets, climate reanalyses, and linearized climate model experiments. A sensitivity analysis across 26 climate-period pairs identifies 1981–2006 (P1) and 2007–2025 (P2) as the periods exhibiting the largest change in the ENSO-rainfall relationship. During P1, ENSO–rainfall correlations were predominantly negative, with patches of weak positive correlations over the western Maritime Continent. During P2, the positive correlations were substantially amplified and spatially expanded, indicating wetter conditions during El Niño when much of the Maritime Continent experiences its wet season. The enhanced wet anomalies were consistent with increased moisture flux convergence over the equatorial Maritime Continent, driven by a weakened western North Pacific anticyclone and a strengthened anticyclone south of Java. Linear baroclinic model experiments suggest that these circulation changes were primarily attributable to changes in ENSO-induced SST anomalies rather than changes in the long-term background climate, with the changes around the Maritime Continent better reproduced when Indian Ocean SST anomalies were incorporated. The nonstationary ENSO-rainfall relationship shows no clear association with decadal-to-interdecadal climate modes but may be related to the increased relationship between El Niño and Ningaloo Niña along the west coast of Australia.