Core Ideas We used MEMD to explore scale‐specific controls of SWC at a 500‐km transect. The largest mean scale of SWC and environmental factors along the transect was 121 km. Precipitation and temperature were large‐scale factors controlling SWC. Elevation and sand were moderate‐scale factors controlling SWC. Clay content was the dominant factor controlling SWC at all scales. Soil water content (SWC) varies both spatially and temporally and is highly controlled by various factors operating at different intensities and scales. In this study, we investigated the scale‐specific controls of SWC along a 500‐km transect using multivariate empirical mode decomposition (MEMD) at 42 sites. Soil water content and six environmental factors were divided into different intrinsic mode functions (IMFs) and residuals to represent different scales. Different values of IMFs for SWC and environmental factors were obtained throughout the whole profile and within five soil layers (0–1, 1–2, 2–3, 3–4, and 4–5 m). The largest scales (i.e., the scales that explain largest portion of variances) of SWC and environmental factors depended on the soil layer from which SWC was involved in MEMD analysis, and they were 272, 126, 134, 126, 117, and 121 km for soil layers from 0 to 1, 1 to 2, 2 to 3, 3 to 4, 4 to 5, and 0 to 5 m, respectively. The residuals accounted for a majority (33–78.1%) of the variance of the original data. At large scales (>250 km), precipitation and temperature were the controlling factors on SWC, whereas at moderate scales (65 km), elevation and sand were the factors determining SWC. In contrast, at all scales, clay content affected SWC distribution. The scale‐specific prediction of SWC on the basis of IMFs and residuals contained more information on environmental factors than the results obtained at the measurement scale. Overall, SWC prediction from IMFs and their residuals were superior to those based on the original data. Using information obtained from MEMD could improve our understanding of the scale‐specific characteristics of soil water and environmental factors across a long transect scale.