The invention relates to a carrier synchronization method in a UFMC system, comprising the following steps: first, generating two sets of orthogonal codes at a sender, inserting the orthogonal codes as pilot sequences into original data, and modulating, filtering and sending the original data through UFMC; then, performing time-domain zero filling and 2N-FFT transform at a receiver, extracting data on even bands, sending the data to a filter matching the sender, getting the estimated value of data information using a zero forcing equalizer, extracting pilot signals and calculating the correlation between the two sets of pilot signals, and minimizing the correlation to achieve UFMC system carrier frequency synchronization; and finally, using an iterative algorithm to improve the accuracy of frequency offset estimation. According to the invention, the carrier frequency offset of the system is estimated by inserting a pilot frequency into each sub band of UFMC, so good properties of the UFMC system are maintained, and the accuracy and stability of frequency offset estimation are improved through iteration. Therefore, the bit error performance of the system is enhanced, the quality of communication is improved, and the design complexity of the filter in the UFMC system is reduced to a certain extent.