The invention discloses a method and a system for obtaining a relation between groundwater and a natural vegetation system. The method comprises the following steps of: determining a vadose zone strata structure boundary of a researched area, wherein the researched area is a drought or semiarid area; acquiring remote sensing data of the researched area; acquiring vegetation coverage data and groundwater depth and hydrochemical characteristic data of the researched area, which are measured in the field; inverting the remote sensing data of the researched area by utilizing a dimidiate pixel model and acquiring a vegetation coverage image in a satellite pixel scale; generating a groundwater depth and hydrochemical characteristic image in a satellite pixel scale; generating a two-dimensional scatter diagram of a relation between the vegetation coverage and the groundwater depth and the hydrochemical concentration in a satellite pixel scale; and acquiring the relation that the natural vegetation growth is changed with the groundwater depth and the hydrochemical concentration. In the relation between the groundwater and the natural vegetation system, hwich is researched by the invention, spatial scales of research objects are matched; and the relation between the ground water and the natural vegetation system can be effectively and deeply disclosed.