Integrated rice-duck farming system (IRDFS) is one of the main practices in traditional Chinese agriculture. IRDFS as shown great effects on rice growth, insect, disease and weed control and paddy biodiversity and environment. However, there is no direct field evidence concerning the impact of IRDFS on rice grain quality. In this study, we examined the impacts of different rice growing techniques on a variety of rice grain qualities and properties, including milling, appearance, cooking, nutrition, and micro element contents through field experiments in Zengcheng Reseach and Education Station, South China Agricultural University in 2005. Treatments consisted in IRDFS, turbid water system, and conventional rice farming system. Our results showed that IRDFS significantly increased the rate of head milled rice, the grain width and the Mn content, but decreased the rice chalkiness, the length/width ratio, and the protein and amino acid contents. No significant impacts were observed on the rates of brown rice and milled rice production nor on the contents of gel consistency and amylose. This study suggests that IRDFS can improve rice grain quality to a certain degree and is an effective ecological technology for high-quality rice production.