The invention discloses a three-dimensional reconstruction method for a soil microstructure. The three-dimensional reconstruction method comprises the following steps: I, acquiring a soil sample: acquiring the soil sample on which three-dimensional reconstruction is required to be performed, wherein the soil sample is a cylindrical soil sample; II, hierarchically scanning the soil sample: hierarchically scanning the soil sample from top to bottom by using a scanning electron microscope, wherein the soil sample is divided into a plurality of scanning surfaces from top to bottom, the scanning electron microscope is adopted during scanning of each scanning surface, and each scanning surface is divided into a plurality of regions for scanning, then a plurality of electron microscope scanning images acquired by scanning are spliced to acquire an entire electron microscope scanning image of the scanning surface; III, sorting the electron microscope scanning images; IV, positioning the images; V, performing three-dimensional reconstruction: calling a three-dimensional reconstruction module to process a plurality of entire electron microscope scanning images to acquire a three-dimensional space model of the soil. The method has the advantages of simple steps, rational design, convenience in implementation and good use effect, and the established soil three-dimensional space model can truly reduce the internal structure of the soil.