The invention provides a remote sensing inversion method for the simultaneous estimation of the relative soil moisture of a root region and surface layer, and belongs to the technical field of soil moisture estimation. The method comprises the following steps of: (A) determining input data required by the method, and constructing an input data set; (B) through calculating the ground surface temperatures of dry bare soil, dry vegetation, wet bare soil and wet vegetation, calculating the critical temperature between sufficient root zone soil moisture/ surface soil moisture deficiency and root zone soil moisture deficiency/surface layer moisture without soil; (C) calculating the relative soil moisture of the root zone and surface layer according to the surface temperatures of the four extremeend members and the critical temperature. According to the method, the surface layer moisture and root zone soil moisture with different contributions to ground surface evaporation are separated frommixed soil moisture, and the simultaneous inversion of the relative soil moisture of the surface layer and root zone is realized, so that the estimation precision of the relative soil moisture of anunderlying surface is improved.