As a typical experimental Soil and Water Conservation District, Yanhe watershed has long been plagued by soil erosion due to severe human disturbances. Exerting remote sensing (RS) and geographic information system (GIS) technology, this paper firstly analyzed and simulated ecological hydrological process in Yanhe watershed based on SWAT model, constructed a comprehensive landscape indices which was closely related to soil erosion, and reflected the coupling relationship between regional landscape pattern change and soil erosion. The results are as follows: (1) Areas of different land use types remained relatively stable from 1990 to 2000 and then changed drastically from 2000 to 2010, which was characterized by lawn expansion and cultivated land shrinkage. (2) In terms of the spatial heterogeneity of hydrological response unit (HRUs), the correlation coefficient of seven selected landscape indices and runoff was very small, and cannot pass all significant testing. But correlation between the indices and sediment yield except for Total Core Area (TCA) and Interspersion and Juxtaposition Index (IJI) was remarkable. (3) According to ‘the source–sink’ theory of soil erosion, new landscape index—slope-HRU landscape index (SHLI) was built, and reflected the relationship between landscape pattern and soil erosion processes to a certain extent. (4) Coupling relationship between SHLI in 2010 and annual sediment was very prominent. In the sub-basin scale, SHLI has obvious regional differentiation from annual sediment.