Based on spectral analysis, a synchronization algorithm modulated multiple pilot symbols using Constant Amplitude Zero Auto-Correlation (CAZAC) sequence was presented for HF OFDM signal acquisition under low signal to noise ration. The fast signal acquisition was realized by time-frequency domain two-dimension estimation, and synchronously the integer frequency shift was obtained by the maximal peak position of spectrum function. Then the phase difference of adjacent pilot symbols was used for precisely fractional frequency shift estimation. Finally, Matlab simulations and on-chip real-time analysis of the algorithm using FPGA were done. The results demonstrated that this algorithm achieves fine performance at low SNR and can work efficiently as a block of an OFDM baseband receiver processor.