Waxy rice is an essential mutant type of rice, which quality is controlled by amylopectin fine structure and apparent amylose content (AAC). The influence of amylopectin structure and AAC on quality and the waxy rice can be obtained by editing the Waxy (Wx) gene have been elucidated. However, the quality of waxy rice cannot be predicted before breeding, especially how to determine the quality of waxy (wx) mutants by wild types (WT) quality remains unclear. Herein, the quality of waxy rice has been successfully predicted through analyzing the association in physicochemical properties before and after Wx gene knockout. We demonstrated that the higher amylose WT would obtain higher amylose wx mutants, and wx mutants were endowed gelatinization temperature, amylopectin chain ratio and agronomic traits similar to WT. These data indicate that the quality of wild varieties played a decisive role in waxy rice breeding. Overall, we provide a new strategy for the specific quality breeding of waxy rice, which can get waxy rice of prescribed quality and contribute to expanding the particular type of waxy rice germplasm resources.