A method and an apparatus for transmitting a signal in a communication system are provided. An information vector is encoded according to a Low Density Parity Check (LDPC) encoding scheme, thereby generating an LDPC codeword. Minimum surviving check nodes are reserved for recovery of punctured nodes in the LDPC codeword. A check node is selected having a smallest cost function from among unreserved check nodes. A variable node is selected being unpunctured and having a smallest cost function from among variable nodes connected to the selected check node. The selected variable node is punctured when the selected variable node is not connected to the reserved check node. A stopping set check is performed when the selected variable node is connected to the reserved check node. The variable node is punctured when the stopping set check has been successfully performed. The check node is selected until there remains no variable node to be punctured and puncturing the variable node.