The invention relates to a cross-layer ARQ (Automatic Repeat Request) method in an LTE-WLAN (Long Term Evolution and Wireless Local Area Network) heterogeneous wireless network system. The cross-layer ARQ method comprises the steps of: respectively adding a virtual network interface card between a terminal of the LTE-WLAN heterogeneous wireless network system and a DLL (Data Link Layer) as well as a network layer of a gateway to virtualize a fixed IP (Internet Protocol) for an application layer at the upper side and shield influences from different physical links of a bottom layer at the lower side; and realizing an ARQ protocol on an IP layer by utilizing a closed loop feedback system. The cross-layer ARQ protocol provided by the invention solves the problems of data packet loss or disordered arrival caused by switching of the terminal in an LTE-WLAN heterogeneous wireless network environment efficiently, prevents the TCP link from entering into a congestion control state and performing a rapid recovery or slow start process to affect the link transmission performance seriously due to the loss or disorder of the data packet. The cross-layer ARQ method in the LTE-WLAN heterogeneous wireless network system, disclosed by the invention, has the advantages of well guaranteeing quality of data transmission between the terminal of the heterogeneous network system and the gateway, providing the transmission layer with reliable services and enabling a terminal user to obtain high-speed and smooth communication experience in the heterogeneous wireless network environment.