A method for preventing choking of a urea injection nozzle in after run operation on a SCR system which supplies urea stored in a urea tank through a supply module, a urea injection nozzle and a urea line connecting the supply module and the urea injection nozzle, the method for preventing choking of a urea injection nozzle includes comparing pressure within the supply module with a first predetermined pressure (Pa), open controlling the urea injection nozzle when the pressure in the supply module is higher than the first predetermined pressure (Pa) or repeating open/close controlling the urea injection nozzle when the pressure in the supply module is lower than the first predetermined pressure (Pa), pressure equilibrium which recovers pressure in the supply module and stopping the after run operation when the balancing pressure is completed.