Provided is a Forward Error Correction (FEC) encoding method of a variable-length packet using a three-dimensional (3D) storage apparatus. In the FEC encoding method, an FEC coding may be performed to calculate a corresponding parity packet while an input data packet is imaginarily connected to the 3D storage apparatus having a predetermined storage width and data area height to be arranged, the calculated parity packet may be stored and arranged in a vertical direction and a depth direction of the 3D storage apparatus, and an expansion data packet including both information for restoration of a data packet and the data packet may be transmitted together with the parity packet.