The invention provides a tunnel connection channel flexible protection apparatus. A connection channel is connected between two adjacent main body tunnels to form a channel port on the main body tunnels. The flexible protection apparatus comprises a door frame and a flexible safety door, wherein the door frame is installed in the channel port position via an arc-shaped installation plate arranged on the back surface; the arc-shaped installation plate is fixedly connected to the inner wall of a pipe sheet of the main body tunnel; an opening is formed in the center of the arc-shaped installation plate; the opening is communicated with the channel port; the flexible safety door can be accommodatingly connected to the top of the door frame; and when the flexible door expands toward the front surface of the door frame, the lateral side of the flexible safety door is closely fixed to the door frame. Separation of the connection channel from the on-construction main body tunnels upon collapse and water permeability during excavation and supporting can be achieved; and safety of the excavation construction of the whole tunnel can be further improved.