Objective To study urodynamic changes of urine at different degrees of hydronephrosis based on computational fluid dynamics (CFD) method, so as evaluate the influence of hydronephrosis degree on kidneys’ ability to discharge stones. Methods Twelve models, including the branched pelvis Model A (normal hydronephrosis A1, mild hydronephrosis A2, medium hydronephrosis A3, severe hydronephrosis A4 models), mature ampullary pelvis Model B (normal hydronephrosis B1, mild hydronephrosis B2, medium hydronephrosis B3, severe hydronephrosis B4 models), and embryo pot abdominal pelvis Model C (normal hydronephrosis C1, mild hydronephrosis C2, medium hydronephrosis C3, severe hydronephrosis C4 models) were established. The urine flow velocity and velocity vector at the neck of the kidney, the outlet of the renal pelvis were calculated by CFD method. Results As the degree of hydronephrosis increased, the flow velocity of urine at the neck of the kidney and the outlet of the renal pelvis decreased. The urinary shearing force of the stones and the kidney’s ability to discharge stones gradually decreased, whereas the circulatory stagnation zone and the velocity boundary layer in kidney aggregate system gradually increased. Conclusions Hydronephrosis can cause changes in urodynamics of the urine. Therefore, the effect of hydronephrosis with different degrees on the patient’s ability to discharge stones after surgery should be fully considered， so as to choose an appropriate treatment method for kidney stones in clinic.