The invention discloses a magnetron sputtering device for preparing a flexible liner membrane. The magnetron sputtering device comprises substrates and target materials, wherein the target materials comprise an upper target material and a lower target material, and the two target materials are oppositely arranged up and down; magnets for a magnetic field between the two target materials are arranged at the upper part of the upper target material and the lower part of the lower target material, and the direction of the magnetic field is perpendicular to the target materials; the substrates are perpendicularly arranged on the outer sides of the two target materials. In the sputtering process, after a secondary electron flies out of target surfaces, the secondary electron is accelerated by the electric field of the cathode of the target materials, the electron is bound by the magnetic field to move to the anode and is effectively closed between the two target poles to do Lorentz movement, and a cylindrical plasma is formed; after electronic energy is exhausted, the electron is finally deposited on the substrates. As the electronic energy is low, the temperature rise of the substrates is low, and the membrane effectively avoids ion damage. Meanwhile, the membrane is formed by target material ion scattering and thermal decomposed deposition, so that the membrane is deposited at the room temperature, the damage of burning and deformation of a flexible liner in the traditional magnetron sputtering process is avoided, and the quality of the membrane is ensured.