This study aims to detect changes in rainfall variability caused by climate change for various scenarios in the CMIP6 (Coupled Model Intercomparison Project Phase 6) multi-model ensemble. Projected changes in rainfall unevenness in terms of different timescale indices using three categories, namely WD50 (number of wettest days for half annual rainfall), SI (seasonality index), and DWR (ratio of dry-season to wet-season rainfall) are analyzed in Zengwen Reservoir watershed, southern Taiwan over near future (2021–2040) and midterm future (2041–2060) relative to the baseline period (1995–2014) under SSP2-4.5 and SSP5-8.5 scenarios. The projected rainfall for both baseline and future periods is derived from 25 GCMs (global climate models). The results indicate that noticeably deteriorated rainfall unevenness is projected in the Zengwen Reservoir watershed over future periods, which include decreased WD50, increased SI, and decreased DWR. Though there were noticeable differences in the rainfall projections by the different GCMs, the overall consensus reveals that uncertainties in future rainfall should not be ignored. In addition, WD50 has the greatest deviated relative change in mean, which implies that the short-timescale rainfall unevenness index is easily affected by climate change in the study area. Distributional changes in rainfall unevenness determined by simultaneously considering alterations in relative changes in mean and standard deviation indicated that there was no single dominant category. However, the top two categories, with summed frequencies exceeding 0.5, characterize different properties of rainfall unevenness indices. The top two categories of WD50 and SI commonly have decreased mean and increased mean, respectively, but nearly equal frequencies of the top two categories in DWR exhibit opposite variations. The proposed rainfall unevenness change detection approach provides a better understanding of the impacts of climate change on rainfall unevenness, which is useful for preparing adaptive mitigation measures for coping with disasters induced by climate change.