The experiment was conducted at the Taidong Base of Shandong Institute of Pomology, Tai’an City, Shandong Province, China, from May to October 2022. Using Fuji Apple Tianhong.2/SH/Malus robusta (M. robusta) as experimental materials, the differences and mechanisms of the effects of non-bagging and bagging cultivation on the growth and changes in some substance content of Fuji apple fruits were studied. The results showed that compared with bagging, non-bagging cultivation increased single fruit weight and decreased fruit shape index, increased fruit sugar content, reduced acid content, and increased taste. It increased the content of vitamin C (VC) and protein in the fruit, increased the types and content of aromatic components in the fruit, significantly increased the activity of sugar- and acid-related enzymes, and improved the antioxidant capacity of the fruit. Compared to bagging cultivation, non-bagging cultivation improved the weight, taste (sugar acid ratio), and aroma of Fuji fruit, which is related to increasing the content of auxin (IAA), cytokinin (ZR), and salicylic acid (SA) and reducing the content of abscisic acid (ABA) in the fruit, as well as increasing the content of medium and trace elements calcium (Ca), iron (Fe), manganese (Mg), and boron (B). One of the mechanisms involved is the significant increase in gene expression related to phenylpropanoid biosynthesis, pentose and glucuronate interconversion, starch and sucrose metabolism, zeatin biosynthesis, microtubules, motor proteins microtubule movement, xyloglucan metabolic process, cell division, and peroxidase activity. In short, non-bagging cultivation is more conducive to improving the intrinsic quality and flavor development of Fuji apples, and one of the mechanisms is that non-bagging cultivation is beneficial for increasing the expression of related genes.