The invention discloses a transport system and a producing method of a sub-vacuum duct in a rail transport system. The transport system of the sub-vacuum duct comprises the sub-vacuum duct and a closed train, wherein the sub-vacuum duct comprises a downslope section of inlet normal atmosphere, a closed section of inlet liquid, a sub-vacuum section, a closed section of outlet liquid and an upslope section of outlet normal atmosphere, the cross section of the duct is in an elliptical shape, silencing materials, force-bearing components, a vent valve, a drain valve, and the like are installed on the duct, the train is an amphibious train, and the body of the train is made of warer-proof materials. The producing method of the sub-vacuum duct comprises the following steps: A. producing the body of the duct; B. installing the vent valve and the drain valve; and C. generating sub-vacuum: producing the duct into a sub-vacuum duct by a method for generating sub-vacuum by pumping liquid. The invention solves the problems of high manufacturing cost of sub-vacuum ducts, inconvenience for passengers to get on and get off the train when the train passes through the sub-vacuum duct and influence on the vacuum state of the duct. Meanwhile, the invention has the advantages of high efficiency, low energy consumption, simple equipment, and the like.