In response to the problem of large frequency errors and reduced communication accuracy in data link communication systems caused by complex electromagnetic environments, a step-by-step carrier synchronization scheme suitable for data link communication systems by combining time-domain correlation technology and frequency-domain transformation methods is proposed. The relevant formulas of the scheme are analyzed and derived, and simulation analysis is conducted on the scheme. Firstly, the advantages and disadvantages of the classic Partial Matched Filtering-Fast Fourier Transform (PMF-FFT) algorithm were analyzed. Based on it, the PMF-FFT algorithm was used to capture and roughly compensate for the frequency of the received signal. Then, the autocorrelation weighted fusion technique was used to finely estimate the frequency offset. The combination of the two algorithms achieved higher accuracy in carrier wave estimation. Through Monte Carlo experiments, it has been verified that compared with traditional single frequency domain estimation or time domain estimation algorithms, this algorithm has higher estimation accuracy and can achieve more reliable digital communication.