The invention proposes a channel estimation method in NAVDAT based on an odd-even alternative pilot frequency sequence, and the method comprises the following steps: (1) inserting a pilot frequency sequence on the subcarrier of each OFDM symbol at equal intervals at an NAVDAT transmission end according to a specific rule; (2) employing the least square method to estimate a channel impulse response at a pilot frequency position at an NAVDAT receiving end; (3) estimating the channel impulse response of the odd number subcarrier of each OFDM symbol through linear interpolation algorithm; (4) estimating all channel impulse responses based on an interpolation algorithm of a low-pas filter. The method makes the most of channel characteristics of adjacent OFDM symbols to estimate the channel impulse response of the odd number subcarrier of each OFDM symbol. Compared with a mode of comb-shaped distribution pilot frequency insertion with the same pilot frequency interval, the method further improves the accuracy of channel estimation under the condition of not reducing the efficiency of data transmission.