The invention relates to the technical field of oil and gas drilling coring, in particular to a self-suction type confining pressure protection coring inner cylinder and an application method thereof. The upper end of a metal inner cylinder of the device is connected with an exhaust joint, the exhaust joint is provided with an exhaust valve, the lower end of the metal inner cylinder is connected with a connecting sleeve, the lower end of the connecting sleeve is connected with a clamp seat, a rock core claw is arranged in the clamp seat, the metal inner cylinder is internally provided with an elastic liner, the elastic liner is in a contracted state in a natural state, and the drift diameter is smaller than the rock core diameter. The self-suction type confining pressure protection coring inner cylinder realizes the whole-process confining pressure protection of the links including rock core drilling, core taking-out and ground treatment on rock cores, the rock core structure damage and the pore fluid loss are reduced, the complete rock core shape is protected, a more realistic rock core sample is obtained, core falling in the drill lifting process can be effectively prevented, the core harvesting rate is ensured, the structure is simple, installation is convenient to achieve, the cost is low, the performance is reliable, the rock core treatment work volume can be reduced, and the field work efficiency is improved.