Disclosed is a method for real-time cutting of digital organ based on a metaball model and a hybrid driving method, including a cutting procedure for driving a model using a position-based dynamics and a meshless method, a cutting mode which begins from a metaball driven by the position-based dynamics, proceeds to a point set driven by the meshless method and then create a new metaball. The method includes: a preprocessing procedure which performs an initialization operation while reading a model file; a deforming procedure which drives a model using a method based on the position-based dynamics; a cutting procedure which drives the model using the hybrid driving method and performs cutting using said cutting mode; and a rendering procedure which renders the model during the second and third procedures.