A method, an upper computer and a system for programming nodes in a bus network are provided. The method comprises: analyzing a program file to be programmed to obtain data of the program file and a storage address corresponding to the data; broadcasting a routing request message and receiving responding messages returned from a plurality of lower computers, each lower computer corresponding to one node in the bus network; analyzing the responding messages to obtain an operating state of each node among the plurality of layers of nodes; receiving a selected node to be programmed, activating the selected node and transmitting the data and the storage address to a single chip microcomputer corresponding to the selected node when the operating state of each node is a forwarding state; and storing corresponding to the selected node the data in a memory of the single chip microcomputer according to the storage address.