Abstract: Using three-line hybrid rice maintainer line, 803B which is of high quality and high combining ability as the nuclear donor, the effects of combining ability on the traits such as rice yield and nitrogen use efficiency were studied by using five kinds of non-sterile cytoplasm. The results show that the cytoplasm effects on rice yield, NUE, NTE and NHI are significantly different. The ability of nitrogen use efficiency is mainly affected by the additive gene effect, and the heritability of nitrogen absorption and utilization in cytoplasm is greater than that in restorer line. JW-cytoplasm is of high GCA and SCA in the related traits on rice yield and nitrogen absorption and utilization. The hybrid rice JW803A/Suhui527 is of better yield and higher nitrogen use efficiency.