The invention discloses a medical image three-dimensional reconstruction method based on neighborhood topology. And loading an original medical image sequence, obtaining a to-be-calibrated image contour line and a contour line image thereof, and constructing four probability parameters to obtain a target threshold. Reading pixel information to construct a cube set, judging the size relationship between the gray values of cube vertexes and a target threshold value, and pre-classifying the cube vertexes into two types of topological similarity and topological change according to vertex distribution characteristics; if topological changes do not exist in the neighborhood of the topological similarity class, a moving cube algorithm is adopted, and if topological changes exist, a transition algorithm of common plane topological consistency processing is adopted; and for the topology change class, a mobile tetrahedron algorithm divided according to a topology specified mode and a topology dissimilar mode is adopted. According to the method, a moving cube algorithm and a moving tetrahedron algorithm are fused, ambiguity of isoline topological connection is avoided, precision is guaranteed, the calculated amount is remarkably reduced, and the online three-dimensional reconstruction speed of a medical image sequence is increased.