Applying the orthogonal matching pursuit (OMP) to estimate the underwater acoustic (UWA) orthogonal frequency division multiplexing (OFDM) channels is attractive because of its high estimation accuracy and low computational cost. However, most existing OMP‐based algorithms suffer the limited estimation accuracy in impulsive noise (IN) cases. Through the studies can be found, only part of channels’ estimation is affected due to the random IN which appears transient and intermittent in time and frequency. Based on this observation, joint time‐frequency OMP (JTF‐OMP) method is proposed, where the estimation of the affected channels benefits adaptively from that of adjacent channels in time or frequency. It is well known that preliminary Doppler scale estimation is key to the subsequent OMP algorithm, which is difficult to deal with due to the IN. To solve this problem, an adaptive Doppler scale estimation (ADSE) method is proposed. It involves generating two shorter identical cyclic prefixes (CPs) for each OFDM symbol, placed before two adjacent OFDM symbols. The repetition pattern can adaptively defend the IN which appears randomly and shortly in time. Simulation results show that the proposed algorithms integrating JTF‐OMP with ADSE can achieve much higher estimation accuracy and better system reliability than the OMP in the IN environment.