The invention discloses a control method and a control system of a compact shelving system which is easy to implement, has a simple structure and is safe and reliable. The method comprises the following steps: detecting current change (sudden change) according to the change of the current of a driving motor when a compact shelving is extruded at a normal operation state; analyzing and detecting through a safety protection unit; and controlling to whether execute an emergency stop operation of the compact shelving or not by the safety protection unit. The control system comprises a safety protection unit and a current detector; and the safety protection unit is used for analyzing and detecting; and the safety protection unit is used for controlling whether the emergency stop operation of the compact shelving is carried out or not. The control system comprises the safety protection unit and a current detector; and the safety protection unit is used for analyzing and detecting a current signal which is output by the current detector, is extruded when the compact shelving is operated or interfere the driving motor to suddenly change.