Two recombinant inbred lines(RILs) populations, one derived from the cross between Zhongyouzao 8(indica) and Toyonishiki(japonica), the other derived from the cross between Qishanzhan(indica) and Akihikari(japonica), were used to identify indica-japonica subspecies differentiation of hybrids by Cheng’s index method and to determine the eating quality and RVA profile characteristic value of rice, to analyze the relationship between cooking-eating quality and subspecies differentiation in RILs populations from indica-japonica crossing. The number of lines from Zhongyouzao 8/Toyonishiki and Qishanzhan/Akihikari are 158 and 142,respectively. The results showed that: 1) Cheng’s index, taste, comprehensive score and RVA characteristics of the two RILs populations followed a continuous distribution, with most lines being mid-parent type. 2) There were insignificant correlations or low correlation coefficients between Cheng’s index and taste, comprehensive score, RVA characteristics. There were insignificant differences among taste, comprehensive score and RVA characteristics for different subspecies based on Cheng’s index. It showed that indica-japonica differentiation had no direct influence on cooking-eating quality. 3) With the rising taste and comprehensive score, hot paste viscosity, cool paste viscosity, setback viscosity, consistence viscosity decreased and breakdown viscosity increased, other RVA characteristics did not change obviously.