The invention relates to a dual-energy focus stack three-dimensional reconstruction method for realizing element space positioning, which comprises the following steps: measuring a full-electron yieldabsorption spectrum of a to-be-detected element in a sample so as to determine absorption edge energy, and selecting edge front energy; scanning and imaging the sample, and acquiring a first focus stack image on a group of absorption edges, wherein the energy of the incident light is the energy of the absorption edges of the element; scanning and imaging the sample, and acquiring a second focus stack image in front of the group of absorption edges, wherein the energy of the incident light is the edge front energy of the element; respectively reconstructing the first focus stack image and thesecond focus stack image by using a focus stack algorithm, and respectively and correspondingly obtaining a first three-dimensional structure diagram and a second three-dimensional structure diagram;and processing the first three-dimensional structure diagram and the second three-dimensional structure diagram through a K-edge subtraction or comparison dual-energy contrast method to obtain the spatial distribution condition of the element in the sample.