In order to resolute the micro-Doppler frequency ambiguity caused by radar pulse repetition frequency not high enough (i.e., pulse dimension does not satisfy the requirement of Nyquist sampling theorem), this paper presents a micro-Doppler frequency ambiguity resolution method based on complex-valued U-net. The echo sequence is interpolated by zeros in the pulse dimension to increase the equivalent pulse repetition frequency, so that the echo sequence after zero interpolation contains the real micro-Doppler frequency; at the same time, some new frequency components are generated. The variation law of the echo sequence frequency after zero interpolation is analyzed. Then, the echo sequence in time domain after zero interpolation is transformed to the time-frequency domain by short-time Fourier transform (STFT). Finally, the time-frequency results can be segmented by the model, which is trained by complex-valued U-net to eliminate the redundant frequencies generated by zero interpolation; thus, the reconstruction of real micro-Doppler frequency is realized. Theoretical analysis and simulation results show that the proposed method can solve the problem of micro-Doppler frequency ambiguity. Compared with fully convolution network (FCN) and fully convolution residual network (FCRN), the proposed method has better performance and robustness.