The invention discloses a double-lined tunnel with an isolation layer structure. The double-lined tunnel with the isolation layer structure comprises a tunnel body and comprises a primary lining and asecondary lining which are distributed in sequence from outside to inside. An isolation layer made of a flexible material is arranged between the primary lining and the secondary lining, and the isolation layer is used for isolating the force of the secondary lining when the primary lining is deformed. The isolation layer is made of polyethylene polymer materials with tensile strength greater than or equal to 3.0MPa, the elasticity modulus greater than or equal to 0.1 Ga and less than or equal to 0.5 Ga, the tensile elongation at break greater than or equal to 20% and glass transition temperature less than or equal to -70DEG C. The double-lined tunnel with the isolation layer structure is simple in structure, convenient and fast in construction and good in waterproof performance, the setting of the isolation layer enables the force of the primary lining and the secondary lining to be more clear, the structural anti-permeability and waterproof capacity of the tunnel is enhanced, and the double-lined tunnel is applicable to engineering fields such as roads, railways, rail transit tunnels and hydraulic tunnels with complex engineering geology, hydrogeology and other construction conditions.