A network grouping system and a network grouping method thereof are provided. The network grouping system includes a controlling server and a connecting server. The connecting server connects to the controlling server via a switch. The connecting server embeds a grouping identifier into a network packet, and transmits the network packet to the controlling server via the switch. The controlling server retrieves the grouping identifier from the network packet, and creates a grouping configuration according to the grouping identifier. The grouping configuration records a matching relation of the grouping identifier with the connecting server. The controlling server further transmits the grouping configuration to the switch so that the switch passes on network packets according to the grouping configuration.