Methods and systems for estimating a surface runoff based on a pixel scale are disclosed. In some embodiments, the method includes the following steps: (1) calculating a vegetation canopy interception water storage, a litterfall interception water storage, and a soil water storage according to an obtained original remote sensing dataset of a climate element in a study area; (2) calculating a vegetation-soil interception water conservation in the study area based on an established vegetation-soil interception water conservation estimation model according to the vegetation canopy interception water storage, the litterfall interception water storage, the soil water storage, and monthly precipitation; and (3) calculating a surface runoff in the study area based on an established water balance water conservation estimation model according to the monthly precipitation, monthly snowmelt, monthly actual evapotranspiration, and the vegetation-soil interception water conservation in the study area.