Understanding the complex variations in water use efficiency (WUE) is critical for optimizing agricultural productivity and resource management. Traditional analytical methods often fail to capture the nonlinear and multiscale variations inherent in WUE, where multifractal theory offers distinct advantages. Given its limited application in WUE studies, this paper analyzes the spatiotemporal characteristics and influencing factors of the WUE in Anhui Province from 2001 to 2022 using a multifractal, multiscale approach. The results indicated that the WUE exhibited significant interannual variation, peaking in summer, especially in August (2.4552 gC·mm⁻¹·m⁻²), with the monthly average showing an inverted “V” shape. Across different spatial and temporal scales, the WUE displayed clear multifractal characteristics. Temporally, the variation in fractal features between years was not prominent, while inter-seasonal variation was most complex in August during summer. Spatially, the most distinct multifractal patterns were observed in hilly and mountainous areas, particularly in regions with brown soil distribution. Rainfall was identified as the primary natural driver influencing regional WUE changes. This study aims to promote the sustainable use of water resources while ensuring the stability of agricultural production within protected farmlands.