Bald patches (BPs) are known to accelerate and simultaneously mitigate the process of desertification. However, the mechanisms of these two synchronous actions are little studied in high desert and cold systems; and the incidence of BPs on alpine meadows degradation in Qinghai-Tibetan Plateau (QTP) of China is still unavailable. This study first aims to investigate the soil properties and the erodibility of the system BPs-VPs at the Beiluhe basin in QTP. Then, we adopted dye tracer and HYDRUS-2/3D methods to interpret the water infiltration patterns from point scale to slope scale. The results show that the mattic epipedon layer on the top soil (0–20cm) of VPs directly reduced the impact of raindrops on alpine meadow; and the adhesion of root system in VPs prevented the soil particles from stripping and washing away by runoff. The soil particles in BPs were easily eroded by rainfall, lowering the ground level of BPs relative to the ground level of VPs. The two patches therefore alternated to form an erosion interface where marginal meadow was likely detached by raindrops and washed away through runoff. The saturated hydraulic conductivity (Ks) of surface soil (0–10 cm) was 124% higher in BPs than the VPs. Thereby, BPs caused a high spatial variation of infiltration and runoff in QTP. Moreover, this difference in Ks between the two patches conducted to a lateral flow from BPs to VPs, and to soil layers with different water contents. These findings highlight that the water flow features can potentially disturb the processes of freezing-thawing, frost heaves, and thaw slump; and accelerate the alpine meadow degradation. Therefore, land cover such as crop and vegetation should be applied over the bare soil surface to prevent the degradation of alpine meadow.