Provided is a system and method for estimating the motion of a target inside a tissue based on surface deformation of the soft tissue. The system consists of an acquisition unit, a reference input unit, two surface extraction units, a target position extraction unit, a feature calculation unit, and a target motion estimation unit. The method includes: the acquisition unit acquires an image Ii of the soft tissue; the surface extraction unit extracts a surface fi of the soft tissue from Ii; the reference input unit acquires a reference image Iref of the soft tissue; the surface extraction unit and the target position extraction unit respectively extract a reference surface fref of the soft tissue and a target reference position tref from Iref, the feature calculation unit calculates deformation feature Ψi of fi relative to fref, the target motion estimation unit estimates the target displacement based on Ψi and tref.