The invention belongs to the technical field of municipal and highway tunnels, and particularly relates to a submarine single-pipe upper-lower layer long municipal and highway shield tunnel ventilation system and method. The system is characterized in that an upper lane and a lower lane are arranged inside a shield tunnel, a civil smoke removal air duct is arranged at the top of each of the upper lane and the lower lane, and smoke removal air shafts connected with the civil smoke removal air duct of the upper lane and the lower lane are arranged at both ends of the shield tunnel; the middle of the shield tunnel is divided into a shield segment A, a shield segment B and a shield segment C sequentially and longitudinally along the tunnel, area of the civil smoke removal air duct of the shield segment A is equal to that of the civil smoke removal air duct of the shield segment C, the area of the civil smoke removal air duct of the shield segment B is 1/5-3/5 of that of the civil smoke removal air duct of the shield segment A, and jet fans are respectively arranged in open excavated and hidden sections at the two ends of the shield segment B and the tunnel. Through the ventilation scheme, dimensional requirements on shield section are met, project implementation difficulty and construction risk are lowered, and cost in engineering construction is saved.