Content of wheat flour proteins affects the quality of wheat flour. Zinc nutrition in wheat can change the protein content of the flour. The inconsistency and instability of wheat grain quality during grain filling while under high temperature stress (HTS) are major problems in the production of high quality wheat. At present, there is a lack of studies on zinc fertilizer and HTS effects on wheat flour protein and the content of its components. For this study, treatment combinations of four levels of zinc fertilizers and exposure to a short-term HTS, at 20 d after flowering (D20), were tested on two wheat cultivars with different gluten levels. Individuals of a strong gluten wheat, Gaoyou 2018 (GY2018), and a medium gluten wheat, Zhongmai 8 (ZM8), were grown in pots at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing in 2015–2017. We measured grain yield and weight and the activities of two enzymes (nitrate reductase and glutamine synthetase) from the flag leaves, collected at D10 and D20. Total protein content, protein yield, and content of four protein components (albumin, gliadin, glutenin, and globulin) were measured from flour produced from the pot-grown plants. HTS significantly increased the contents of total protein, albumin, gliadin, and glutenin in wheat grains, and reduced the grain yield, grain weight, protein yield, globulin content, and flag leaf nitrate reductase (NR) and glutamine synthetase (GS) activities. The results showed that HTS and zinc fertilizer had greater impacts on the strong gluten cultivar compared to the medium gluten cultivar. Under HTS, grain yield decreased by 13 and 8% in GY2018 and ZM8, respectively; protein yield decreased by 7 and 8% in GY2018 and ZM8, respectively. Zinc fertilizer increased: grain and protein yields; grain weight; total protein, albumin, gliadin, and glutenin contents; protein yield; and NR and GS activities. In contrast, zinc fertilizer reduced the content of globulin. The addition of 15 mg Zn kg–1 soil had the strongest effect on grain yield and quality as compared to the other three treatments (additions of 0, 30, and 45 mg Zn kg–1 soil). Zinc fertilizer also reduced the negative effects of HTS on protein yield, content, and components’ content. Therefore, wheat grown with additional zinc in the soil can improve the quality of the flour.