The purpose of the invention is to provide a method for decision of secondary channel equalization of underwater acoustic OFDM. According to the method, a CombMMSE channel estimation is carried out; once equalization is carried out on received data by utilizing a frequency response to obtain post-once equalization data; de-mapping processing is carried out on subcarriers of the post-once equalization data and then estimation of original data is obtained by convolutional decoding or Turbo decoding; coding is again carried out on the decoded data according to an original encoding rule to obtain post-secondary coding data; estimation on block pilot frequency is obtained by taking the estimated data subcarriers as a training sequence and by combining comb pilot frequency subcarriers, so that all subchannels have training data; and then secondary channel estimation is again carried out by utilizing a BlockMMSE algorithm. According to the invention, comb pilot frequency interpolation errors can be substantially reduced; moreover, a good balancing effect can be achieved on the condition that an interval between pilot frequencies is big.