Highlights What are the main findings? Data fusion and assimilation technology were employed for the retrieval of soil moisture at various soil depths. The depth-dependent variations, stability differences, and lagged rainfall responses of soil moisture from shallow to root-zone layers are revealed. What is the implication of the main finding? A reliable data foundation for layered soil moisture monitoring is provided. The understanding of soil moisture dynamics and rainfall-driven regulation processes in the ecotone from the Qinghai-Tibetan Plateau to the Loess Plateau is enhanced.Highlights What are the main findings? Data fusion and assimilation technology were employed for the retrieval of soil moisture at various soil depths. The depth-dependent variations, stability differences, and lagged rainfall responses of soil moisture from shallow to root-zone layers are revealed. What is the implication of the main finding? A reliable data foundation for layered soil moisture monitoring is provided. The understanding of soil moisture dynamics and rainfall-driven regulation processes in the ecotone from the Qinghai-Tibetan Plateau to the Loess Plateau is enhanced.Abstract Focusing on the ecotone from the Qinghai-Tibetan Plateau to the Loess Plateau (QPtoLP), this study firstly constructs a retrieval model of soil moisture in various depth layers based on multi-source remote sensing data by using the two-source energy balance (TSEB) model and soil-vegetation-atmosphere transfer (SVAT) model. And then, it uncovers how the soil moisture changes across various depths in the root zone and discusses the lagging effect of rainfall. This research indicated that the correlation between the retrieved soil moisture and field-monitored values in various depth layers ranged from 0.720 to 0.8414, demonstrating that it is suitable for the retrieval of soil moisture at various depths in the study area. During the growing season, soil moisture experienced a slight decrease from mid-May to mid-June, followed by a partial recovery in mid-June. After a dry spell in July, the soil moisture reached its lowest point, but surface and deep soil moisture levels rebounded to above 0.2 and 0.1 cm3/cm3, respectively, by mid-August. Spatially, the soil moisture was higher in the southern region, characterized by dense human activities, and lower in the northern region, which is dominated by alpine grasslands. Comparing different depths, the soil moisture at a 0-5 cm depth was generally the highest most of the time, except in July, when the 35-50 cm depth had the highest value. Additionally, the surface soil moisture at a 0-5 cm depth indicated frequent fluctuations at elevations above 4000 m. As the soil depth increases, the rainfall lag effect becomes more pronounced, and the lag effect in the 35-50 cm soil layer is three days.