An EtherCAT-based network system configured to change a PDO list set, and an operation method thereof are provided, the system including at least one or more slave devices, a master device configured to connect and operate the slave device in response to an operating transmission PDO list or an operating reception PDO list provided from outside, and a host computer configured to extract the operating transmission PDO list or the operating reception PDO list from information file of the slave device and provide to the master device, wherein the information file includes at least one of identity information of the slave device, PDO list item changeable information, at least one or more transmission PDO list, and at least one or more reception PDO list.