Sediment transport is a multi-scale and non-linear process controlled by multiple variables. Given the intricate nature of sediment transport mechanisms and the overlap of different factors’ effects on it at various time scales, unraveling the relationship between sediment load and its influencing factors is challenging. This study aimed to elucidate the multi-timescale effects of factors on monthly suspended sediment load in a seasonal inland river. In this study, monthly sediment loads measured by the depth-integrating method were obtained from the Tabu River Basin in northern China from 2007 to 2021, alongside data on four controlling factors: runoff, precipitation, water surface evaporation, and the normalized difference vegetation index (NDVI). The results showed that sediment load, runoff, and precipitation showed strong variability during 2007–2021, while water surface evaporation and NDVI exhibited moderate variability. Multivariate empirical mode decomposition (MEMD) decomposed the temporal patterns of sediment load and associated variables into five intrinsic mode functions (IMF) and a residue. IMF1 (4.7 months), IMF2 (9.0 months) and IMF3 (14.2 months) collectively explained 115.88 %, 91.73 %, 91.28 %, 107.69 %, and 106.09 % of the total variability in sediment load, runoff, precipitation, water surface evaporation, and NDVI, respectively. Subsequently, the time-dependent intrinsic correlation (TDIC) was utilized to illustrate the inherent relationships between sediment load and its controlling factors across various time scales. The associations between sediment load and the controlling factors changed significantly with the scale. Runoff was the dominant factor controlling sediment load at IMF1 (4.7 months), IMF2 (9.0 months), IMF3 (14.2 months), and IMF4 (25.1 months). Water surface evaporation controlled the sediment transport process at IMF5 (63.6 months). The prediction of sediment load on the measurement scale, using scale-specific controls analyzed with MEMD (R2 = 0.993), demonstrated superior performance compared to traditional multiple linear regression prediction (R2 = 0.748). This study will provide a theoretical basis for effective prevention and control of soil erosion and watershed management in inland river basins.