Wheat flours milled from five different varieties of wheat and collected at an extraction rate of 60% were used as raw materials in this study. The proximate compositions, dough Farinographic and Extensographic properties, and the quality indices of deep-fried gluten balls prepared from these flours were measured. The proteins of these five different wheat flours were extracted and analyzed using the electrophoretic method, and the effect of protein composition on the quality of deep-fried gluten balls prepared from these flours was investigated. In this study, the proteins in each sample were divided into six groups, and the molecular weights of the proteins in these six groups are as follows: (I) 205.0–97.4kDa; (II) 97.4–66.2kDa; (III) 66.2–45.0kDa; (IV) 45.0–36.0kDa; (V) 24.0–19.7kDa; (VI) 14.4–6.5kDa, respectively. The results show that the protein contents of groups I, II, and V are negatively correlated to peak force and Hunter b value of deep-fried gluten balls, but positively correlated to Hunter L value and sensory evaluation score of appearance. The above results reveal that the high-molecular weight glutenin subunits, ω-gliadins, and albumins/globulins of wheat flour have a profound effect on the quality of deep-fried gluten balls.