Long-term quantification of the migration loads of subsurface runoff (SSR) and its collateral soil nutrients among different soil layers are still restricted by the runoff collection method. This study tested the reliability of the U-trough collection methods (UCM), compared with the seepage plate collection method (SPM), in monitoring the runoff, sediment and nutrient migration loads from different soil layers (L1: 0–20 cm depth; L2: 20–40 cm depth; L3: 40–60 cm depth) for two calendar years under natural rainfall events. The results suggested that the U-trough could collect nearly 10 times the SSR sample volume of the seepage plate and keep the sampling probability more than 95% at each soil layer. The annual SSR flux from L1 to L3 was 403.4 mm, 271.9 mm, and 237.4 mm under the UCM, 14.35%, 10.56%, and 8.41% lower than those under the SPM, respectively. The annual net migration loads of sediment, TN, and TP from the L1 layer under the UCM were 49.562 t/km2, 19.113 t/km2 and 0.291 t/km2, and 86.62%, 41.21% and 81.78% of them were intercepted by the subsoil layers (L2 and L3), respectively. While their migration loads under the SPM were 48.708 t/km2, 22.342 t/km2 and 0.291 t/km2, and 88.24%, 53.06% and 80.42% of them were intercepted, respectively. Under both methods, the average leached total n (TN), total p (TP) concentrations per rainfall event and their annual migrated loads at each soil layer showed no significant difference. In conclusion, the UCM was a reliable quantitative method for subsurface runoff, sediment, and soil nutrient migration loads from diverse soil layers of purple soil sloping cultivated lands. Further studies are needed to testify the availability in other lands.