Weighted fractional Fourier transform encrypted chaotic direct sequence spread spectrum (WFRFT-CD3S) signal is aperiodic and complex Gaussian distributed. The aperiodicity and complex Gaussian distribution are conducive to the covert transmission of information but also make it difficult to acquire the WFRFT-CD3S signal. An acquisition method implemented in two steps is proposed to acquire the Doppler-shifted WFRFT-CD3S signal. First, a bidirectional correlation search method is proposed to align the received signal with the local spreading sequence in the time domain. The correlation peak attenuation caused by the Doppler frequency shift is eliminated by differential. Second, the accumulated phase angle caused by the Doppler frequency shift is obtained by the differential correlation value between the aligned received signal and the local spreading sequence. Then, the Doppler frequency shift is estimated by the accumulated phase angle. The detection probability, the false alarm probability, and the root mean square error (RMSE) of the Doppler shift estimation are analyzed theoretically and simulated. The theoretical results are verified by simulation. Theoretical results and simulations show that the detection probability is higher than 0.999, the false alarm probability is less than 0.001, and the RMSE of Doppler shift estimation is lower than 63 Hz when the signal-to-noise ratio is higher than -7.3 dB.