The optimal order in fractional Fourier transform (FrFT) can be used to estimate chromatic dispersion (CD) and nonlinearity in an optical fiber transmission system. In this paper, we propose a novel method to estimate CD with lower computation complexity in fractional domain. The computation complexity can be reduced by 10<sup>3</sup> times with the same measurement accuracy compared with one step method when the number of samples is 8192 and search step is 0.0001. The correctness of the novel method for optimal order searching is proved by chirp parameter estimation for linear frequency modulation (LFM) signals. The measurement relative error is only 0.02%. For CD estimation, the maximum estimation error ratio is 0.338% and 0.564% for 28Gbit/s quadrature phase-shift keying (QPSK) and 16 quadrature amplitude modulation (16QAM) optical fiber transmission systems over 100 km~2000 km SSMF.