The invention discloses an on-board network system and a backbone node message processing method thereof. In the system, a mixed layered network structure of combining a ratio Mesh backbone network and a heterogeneous access network is adopted, and the interconnection of various access networks is realized through an on-board backbone network, thereby the flexibility and the expandability of the system are improved. Meanwhile, a backbone node message processing method is adopted in the comprehensive message processing system of backbone network nodes. The method realizes the transformation of heterogeneous messages between a core network and an edge network, and a publishment/subscription mechanism based information distribution service is adopted, thereby the resource utilization ratio and the information access efficiency in complicated network environment are improved. The invention has military and civil values and particularly has wide application prospects in the fields of airborne command collaborative constellation of military integration information grids, civil aviation networked communication, navigation, monitoring, and the like.