When the fractional Fourier transform (FRFT) is introduced into the weak and high-dynamic global navigation satellite system (GNSS) signal acquisition, the 2-D search cell will be transferred to a 3-D one with respect to the code chip, the Doppler shift, and the Doppler rate. The proper determinations of the code bin and Doppler shift bin in the acquisition process have already been covered in the previous researches. The aim of this paper is to provide an exhaustive analysis of the approach to specify an optimal FRFT order bin, in terms of the Doppler shift rate. The lower and upper bound of FRFT order ranges is determined by the incoming signal dynamics. Then, we propose a precise model to yield an optimal FRFT order bin. Besides, a novel and fast Doppler estimator based on the non-linear least square (NLS) method is presented to improve the performance of the digital FRFT implementation. Finally, an alternate search procedure is proposed to reduce the singular estimations of the NLS method. The simulating examples demonstrate the performance of the proposed algorithms. It has been verified that the computation efficiency and the estimation accuracy have been significantly improved by proposed techniques. INDEX TERMS Global navigation satellite system (GNSS) signal, linear frequency modulation (LFM), fractional Fourier transform (FRFT) order, acquisition, Doppler rate, non-linear least square (NLS).