A network communication method, a system and a controller of PCIe and Ethernet hybrid networks are provided. In one example of the network communication method, a packet is transmitted or received via a network interface (NIC). The packet is transmitted via an Ethernet over PCIe (EoP) port by adopting a PCIe based EoP architecture based on a PCIe bus for an intra-rack transmission, and the packet is transmitted via an Ethernet port for an inter-rack transmission. If the transmitted packet belongs to a broadcast packet, the network interface receiving the packet discards the packet or transmits the packet to the controller without re-broadcasting the packet again.