The invention discloses an organization deformation simulation system and method based on deep learning and finite element modeling, and the system and method utilizes the advantages of the finite element modeling, and reduces the calculation amount of modeling and simulation through a deep learning method. The system comprises an image acquisition device and a processor, the image acquisition device is used for acquiring an original image and a target image and transmitting the original image and the target image to the processor; the processor is used for selecting the interested regions ofthe original image and the target image, and establishing an original three-dimensional finite element model and a target deformation three-dimensional finite element model, performing three-dimensional registration to obtain a rotation translation matrix between the original three-dimensional finite element model and the target deformation finite element model, performing finite element analysison the rotation translation matrix, extracting the finite element characteristics and simulating a target deformation tissue three-dimensional model.