A method and apparatus for controlling mobile early data transmission (EDT) procedure in a wireless communication system is provided. A first core network node, in a wireless communication, receives, from a second core network node, a message for a downlink Data including a size of the downlink data. The first core network node determines whether to initiate an early data transmission (EDT) procedure for the downlink data based on the size of the downlink data. The first core network node transmits, to a radio access network (RAN) node, a paging message including information related to the EDT procedure for the downlink data based on the decision to initiate the EDT procedure for a wireless device.