Provided are a sub-carrier estimation method in a multi-carrier communication system and an apparatus. The method includes: receiving a data frame transmitted by a transmitting end, and extracting a training sequence from the data frame; performing fast Fourier transform operation on the training sequence and a preset reference sequence, respectively, to obtain frequency domain data of the training sequence and frequency domain data of the reference sequence, and conjugately multiplying the two kinds of frequency domain data; extracting real part of conjugate multiplication result; averaging values in each column of an M×N array, respectively, to obtain an output array of 1 row and N columns; and estimating, according to the value in each column of the output array of 1 row and N columns, whether valid data is transmitted over N sub-carriers corresponding to the output array of 1 row and N columns.