Acid rain is a worldwide important environmental problem, and might be a long-term trouble due to the rapid development of industry. The south area of Yangtze River is one major acid rain region in China, where crop production is severely limited by acid rain interacted with acid red soil. Wheat is the third largest crop in China and the second largest crop in Jiangsu province. Both yield and quality of wheat are of importance to food security. Wheat may suffer from acid rain stress during the whole stage, but the later growth stage of grain filling is more critical in determining grain yield and quality. Although the growth and physiological characteristics of crops exposed to acid rain have been broadly studied, little is known about the effect of acid rain on wheat quality. Here, effects of acid rain on wheat yield and quality in wheat were investigated. Two wheat (Triticum aestivum) cultivars of Ningmai 13 and Xumai 31 were selected in a pot experiment in Pailou experiment station in Nanjing Agricultural University, Jiangsu Province, China. Two acid rain treatments, i.e. by spraying solution of pH 2.0 and pH 4.0 were implemented, and that at pH 6.0 was set as control. Acid rain inhibited the growth of wheat. The dry weight of leaf, stem and ear under both acid rain treatments all were reduced as compared with the control. Grain number per spike and yield per shoot of Ningmai 13 was significantly reduced by 48.6% and 56.9% due to acid rain of pH 2.0 as compared with pH 6.0, respectively, and those of Xumai 31 was significantly reduced by 31.2% and 40.1%. As to wheat grain quality, the influence of acid rain was more complicated. Contents of amino acids in wheat grain of Ningmai 13 and Xumai 31 under acid rain of pH 2.0 increased 36.6% and 30.9%, respectively, as compared with control. The content of total protein in grains of Ningmai 13 and Xumai 31 under acid rain of pH 2.0 increased 20.6% and 15.1%, respectively. Acid rain increased contents of albumin and globulin, while decreased content of glutenin and the ratio of glutenin to gliadin. Compared with the control, the albumin content at pH 2.0 in Ningmai 13 and Xumai 31 increased 13.1% and 23.9%, respectively, and the globulin content at pH 2.0 in Ningmai 13 and Xumai 31 increased 35.7% and 100%, respectively. The other protein was also increased by acid rain. While glutenin content at pH 2.0 in Ningmai 13 and Xumai 31 decreased 4.4% and 15.2%, respectively, as compared with the control. Acid rain decreased contents of soluble sugar, starch and fat in wheat grain. The total starch content of Ningmai 13 and Xumai 31 under acid rain of pH 2.0 decreased 11.8% (P<0.05) and 20.2% (P<0.05), respectively. Acid rain also reduced amylopectin content, but has little effect on amylose content. As a result, the ratio of amylopectin to amylose was also decreased, although the difference was not significant. It is concluded that acid rain influenced both wheat yield and quality. Although acid rain enhanced protein content, grain quality was negatively affected as exemplified by the decreased glutenin content and ratio of glutenin to gliadin and amylopectin to amylose.