The present invention relates to a system for controlling urea injection of a selective catalyst reduction apparatus for controlling an injection amount by considering vaporization and resolution characteristics of a urea solution according to driving conditions. Also, the method for controlling urea injection of the selective catalyst reduction apparatus may include determining a necessary ammonia amount according to a predetermined driving condition, determining a necessary urea solution amount by applying an ammonia conversion coefficient of urea solution, and determining a final urea solution amount that is to be finally injected by applying a wall-wetted urea solution amount.