Tillage practices change microtopography and hydrological process, which significantly affects soil erosion. The objective of this study is understanding storm-driven microtopography development under different tillage practices and its effects on runoff and soil erosion. A series of simulated rainfall experiments with an intensity of 2.0 mm min−1 were implemented on three 4 m by 0.8 m soil boxes on a 15° slope with different tillage-induced microreliefs including smooth slope (SS), artificial digging (AD), and ridge tillage (RT). The Hilbert-Huang transform (HHT) was used to detect the change trends of runoff and sediment yield, and the time-dependent intrinsic correlation (TDIC) was used to depict intrinsic runoff-sediment relations. The results showed the soil roughness were SS < AD < RT during different rill erosive stages. AD and RT slopes reduced runoff by 11.5–64.5% compared with the SS slope during water erosion. AD and RT slopes also reduced sediment yield by 13.3–83.4% during interrill erosion process, but the sediment yield increased by 59.2–132.1% during rill erosion. Runoff and sediment yield had multi-scale temporal variation characteristics. Ensemble empirical mode decomposition (EEMD) was adapted to decompose the runoff and sediment yield data into different intrinsic mode functions (IMFs). For the high-frequency components (IMF1-IMF3), rougher microrelief led to increase in the periods of runoff and sediment yield, while the trend of the low-frequency components (IMF4-IMF5) was opposite to that of the high-frequency components. This phenomenon was mainly related to the spatial structure of microtopography. Tillage-induced microtopography altered the associations of runoff with sediment yield in different time scales. This study provided new insights into revealing the mechanism of tillage erosion in sloping farmland.