An RNA separation method includes injecting a reaction solution into a reaction region which contains a covalent linking of specific RNA probe for hybridizing with the reaction solution; adjusting a moderate hybridization temperature in the reaction region; moving the remainder of the reaction solution to a transition region by using a pneumatic actuator; adding a buffer solution to the reaction region, and heating the reaction region to a moderate denature temperature by a heating apparatus; moving a waste solution which is product produced from the reaction region after denature to a waste region by using the pneumatic actuator; and moving the remainder solution back to the reaction region by the pneumatic actuator.