A method for operating a Low Density Parity Check (LDPC) decoder includes assigning each symbol of a codeword as a variable node value for each of a plurality of variable nodes, performing syndrome checking on each check node based on a parity check matrix, calculating flipping function values of the variable nodes based on syndrome values of check nodes and a flipping function, dividing the flipping function values into a plurality of groups, determining a flipping function threshold value based on a group maximum value of a group among the groups, and selectively flipping a variable node value based on a comparison result of a flipping function value of corresponding variable node and the determined flipping function threshold value.