In this paper, we propose a low-complexity channel estimation scheme of affine frequency division multiplexing (AFDM) based on generalized complex exponential basis expansion model (GCE-BEM) over doubly selective channels. The GCE-BEM is used to solve fractional Doppler dispersion while significantly reducing the computational complexity of exhaustive search. Then, the closed-form expression of channel estimation error is derived for the minimum mean square error (MMSE) estimation algorithm. Based on the estimated channel, the MMSE detection is adopt to characterize the impacts of estimated channel on bit error rate (BER) by deriving the theoretical lower bound. Finally, numerical results demonstrate that the proposed scheme effectively mitigates severe inter-Doppler interference (IDoI). Our theoretical performance an alysis can perfectly match the Monte-Carlo results, validating the effectiveness of our proposed channel estimation based on GCE-BEM.