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Zinc (Zn) stress adversely affects the growth of wheat seedlings. Chitosan (CTS), a growth regulator, can mitigate stress-induced damage in plants. This study aims to investigate the alleviating effects of chitosan on zinc stress in wheat seedlings. A hydroponic experiment was conducted to examine the impact of various concentrations of exogenous chitosan (0, 25, 50, 100, 200, and 400 mg·L−1) on the physiological and biochemical characteristics of wheat seedlings under Zn stress (500 µmol·L−1). Chitosan enhanced biomass accumulation, root morphology, chlorophyll content, photosynthetic parameters, the ascorbate-glutathione (AsA-GSH) cycle, antioxidant enzyme activity, and soluble protein content in wheat seedlings, while reducing malondialdehyde (MDA) levels and Zn translocation to the above-ground parts. Additionally, partial least squares (PLS) analysis identified zinc accumulation as a key factor in wheat seedlings’ response to Zn stress. Specifically, 100 mg·L−1CTS increased the tolerance index of shoots and roots by 30.59% and 47.90%, respectively, and significantly reduced oxidative damage caused by Zn stress. The study recommends using 100 mg·L−1CTS as an effective exogenous treatment to enhance zinc stress tolerance in wheat seedlings.