Aqueous two-phase system (ATPS) is regarded as an effective and eco-friendly technique to extract some bioactive compounds. In order to promote the added value and reduce the discharge in the industrial processing of apricot kernels, the aqueous two-phase extraction conditions were optimized with the evaluation of the distribution coefficient (K), ratio of volume (R) and extraction yield (Y) to obtain a higher extraction of amygdalin from the debitterizing water concentrate (DWC) in this paper. The results indicate that the optimal conditions were as follows: 30% (w/w) ethanol and 20% (w/w) ammonium sulfate of the ATPS, at 35°C and pH of 7. Under these conditions, the highest extraction yield was 90.37% and the purity could be increased by more than two times. In a word, the ATPS can be considered as an effective method to recycle the amygdalin from the DWC in the apricot kernels processing.