The Wx gene primarily influences the physiochemical properties changes of rice (Oryza sativa L.) To improve the grain qualities of the cv. Y58S with low amylose content (AC) value, the genetic effect of Wx gene was explored on quality traits. With the BC3F2 genetic population of Y58S line associated with different AC value as the materials, this study reported the genetic effect of three different Wx alleles (Wxª, Wx in, Wx b) under near-isogenic background. It was shown that Wx had major effects on the quality traits, and the genetic effect value was in the order Wxª &gt; Wx in &gt; Wx b. In addition, during the course of physiochemical properties changes of higher AC rice cultivars determined by Wxª or Wx in allele, accompanied by the increasing of AC, gel consistency and head milled rice recovery would be decreased in combination with the rising of chalky traits, all of which resulted in substantial fluctuations on quality traits (p < 0.01). However, the genetic law was not evident for Wx b allele. Therefore, except for the major gene Wx, the minor genes in the regulative network of starch-synthesis might be utilized for quality improvement.