Recently, acid rain has become a serious environmental problem in China. Acid precipitation has occurred in about 40% of the entire area, especially in the rapidly developing industrial regions, such as the many areas around the Yangtze River. Acid rain is formed when sulfur dioxide (SO₂) and nitrogen oxides (NO_x) react with water in the atmosphere to produce H₂SO₄ and HNO₃ and deposit as acid precipitation. Most studies have focused on the effect of acid rain on seed germination, plant morphology, plant carbon metabolism, and grain yield. However, the impacts of acid rain on plant nitrogen and sulfur metabolisms and grain quality have rarely been investigated, although SO₄^2- and NO₃^-are known to be the main components of acid rain. Wheat (Triticum aestivum L.) is a staple food and plays an important role in food security. It is sensitive to biotic and abiotic stresses from flowering to maturity. In this study, a pot experiment was performed to determine the effects of spraying of acid rain with varying acidities (pH, 2.5, 4.0, and 5.6) after anthesis on the activities of key enzymes related to nitrogen and sulfur metabolisms and amino acid and protein contents in wheat grains. Two winter wheat cultivars (Yangmai 15 and Wennong 17) were used in this study. The results showed that acid rain inhibited nitrate reductase activity and decreased the soluble protein content of leaves. At 10 days after anthesis, the soluble protein content in Wennong 17 and Yangmai 15 subjected to acid rain (pH 2.5) decreased by 26.58% (P < 0.05) and 21.31% (P < 0.05), respectively, compared with that in the control. Glutamine synthetase activity in the leaves was increased in Yangmai 15 during the entire grain filling stage and in Wennong 17 only during the late grain filling stage. Acid rain gradually decreased the free amino acid content from the beginning of grain filling stage up to the later stages. The contents of protein and most essential amino acids in mature gains were increased by acid rain and were the highest after treatment with acid rain of higher pH. Acid rain increased the activities of serine acetyltransferase and O-acetylserine(thiol)lyase in Yangmai 15, but had little effect on the activity of key enzymes related to sulfur metabolism in Wennong 17. Acid rain treatment also increased the contents of disulfide bonds and amino acids containing sulfur in the wheat grains of both the cultivars. Thus, acid rain had different influences on wheat sulfur and nitrogen metabolisms, thereby affecting the protein content and composition of wheat grains, and thus its nutritional quality.