The invention relates to a soft tissue deformation simulation method based on a subspace agglomerative algorithm. The method includes steps: a) performing data preprocessing and three-dimensional reconstruction of a soft tissue model; b) conducting a soft tissue biomechanical characteristic analysis; c) realizing collision detection by employing combination of intersection of an AABB bounding boxand triangular patches; and d) finally completing soft tissue deformation simulation calculation through the subspace agglomerative algorithm, realizing space mapping by employing a space nuclear method, and separating an optimal pure subspace by employing a greedy algorithm and a two-dimensional separating algorithm. According to the method, with the combination of the soft tissue three-dimensional geometric modeling and the real-time collision detection method, the soft tissue deformation simulation is performed by finally adopting the improved subspace agglomerative algorithm, the balance between authenticity and timeliness in a soft tissue deformation process can be well adjusted, the phenomenon of distortion or pause of the model in the deformation process is prevented, good simulation effect can be achieved through analysis, the spent time is short, and an important guiding effect is achieved for deformation simulation in virtual operations.