Integrated rice-duck farming system (IRDFS) is one of the cream practices in traditional Chinese agriculture. As a sustainable and ecological mode in rice production, the IRDFS has shown great impacts on rice growth, control of insect, disease and weed, biodiversity, and paddy environment. However, there is no direct field evidence concerning the impacts of the 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 microelement contents through field experiments in Zengcheng Research and Education Station, South China Agricultural University, Guangdong Province, China in 2005. The treatments included the 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 contents of protein and amino acid. No significant impacts were observed on the rates of brown rice and milled rice production and 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.