In military frequency hopping orthogonal frequency division multiplexing (FH-OFDM) application above sea surface, a joint synchronization and channel estimation algorithm based on recursive least square was proposed to improve bit error rate (BER) performance of aircraft communication receiver under different sea conditions. Frequency hopping synchronization was completed by parallel detection. Inter-carrier interference (ICI) of baseband signal was compensated in time domain. With the help of proposed frequency hopping frame structure in slow time-varying channel, a cost function with linear error was formulated to estimate channel’s impulse response (CIR), carrier frequency offset (CFO) and sampling frequency offset (SFO). Estimation of parameters’ initial values was improved by new maximum likehood cost function. Balance expression among bandwidth efficiency, frequency hopping rate and subcarrier numbers was presented. Simulation results showed that the proposed algorithm has better estimation mean square error and BER performance than conventional algorithm under calm sea condition and rough sea condition.