Method for modelling blood vessels includes: obtaining medical imaging data of the blood vessels; generating a three-dimensional personalized model of the blood vessels, based on the medical imaging data; generating a three-dimensional reference model of the blood vessels that reflects a state of healthy blood vessels that lack lesions, based on the medical imaging data or based on numerical reconstruction of the personalized model; performing a numerical simulation of blood flow for the same physical and boundary conditions in the personalized model and in the reference model, the simulation comprising determining conditions of blood flow at an inlet to the blood vessels model and calculating blood flow energy for the inlet and all outlets of the blood vessels model; comparing the blood flow energy measured for the personalized model and for the reference model; determining flow energy change indexes of the blood flow in the personalized model and the reference model.