Increased attention directed at frozen soil hydrology has been prompted by climate change. In spite of an increasing number of field measurements and modeling studies, the impact of frozen soil on hydrological processes at the catchment scale is still unclear. However, frozen soil hydrology models have mostly been developed based on a bottom-up approach, i.e., by aggregating prior knowledge at the pixel scale, which is an approach notoriously suffering from equifinality and data scarcity. Therefore, in this study, we explore the impact of frozen soil at the catchment scale, following a top-down approach, implying the following sequence: expert-driven data analysis → qualitative perceptual model → quantitative conceptual model → testing of model realism. The complex mountainous Hulu catchment, northeast of the Qinghai-Tibet Plateau (QTP), was selected as the study site. First, we diagnosed the impact of frozen soil on catchment hydrology, based on multi-source field observations, model discrepancy, and our expert knowledge. The following two new typical hydrograph properties were identified: The low runoff in the early thawing season (LRET) and the discontinuous baseflow recession (DBR). Second, we developed a perceptual frozen soil hydrological model to explain the LRET and DBR properties. Third, based on the perceptual model and a landscape-based modeling framework (FLEX-Topo), a semi-distributed conceptual frozen soil hydrological model (FLEX-Topo-FS) was developed. The results demonstrate that the FLEX-Topo-FS model can represent the effect of soil freeze-Thaw processes on hydrologic connectivity and groundwater discharge and significantly improve hydrograph simulation, including the LRET and DBR events. Furthermore, its realism was confirmed by alternative multi-source and multi-scale observations, particularly the freezing and thawing front in the soil, the lower limit of permafrost, and the trends in groundwater level variation. To the best of our knowledge, this study is the first report of LRET and DBR processes in a mountainous frozen soil catchment. The FLEX-Topo-FS model is a novel conceptual frozen soil hydrological model which represents these complex processes and has the potential for wider use in the vast QTP and other cold mountainous regions.