In order to investigate the genetic effect of allelic variation of Wx and SSⅢ2 on rice quality, we used a F₃ population, which came from a hybrid combination of indica restorer line CG133R with high amylose content and a glutinous rice variety‘javanica 22’. And plants with polymorphism on Wx and SSⅢ2 loci in the F₃ population were selected as materials. Furthermore, the physicochemical indexes and RVA profile characteristics of each material were analyzed. The results showed that: (1) the first intron polymorphism of Wx had a significant effect on AAC at 0.01 level under background of type I of SSⅢ2. When SSⅢ2 was type Ⅱ, the first intron polymorphism of Wx had a significant effect on AAC and PaT at 0.01 level. (2) SSⅢ2 had no significant effect on rice quality under background of Wx^a. However, there had significant difference on GT and PKV, BDV and PaT of RVA profile at 0.01 level under background of Wx^b. (3) Interaction of Wx and SSⅢ2 had significant effect on rice AAC, GT, PKV, BDV and PaT at 0.01 level. Therefore, Wx had interaction with SSⅢ2, and Wx was dominant epistatic to SSⅢ2. The expression of Wx masked the expression of SSⅢ2.