The concurrence of heat stress of different spells at the cotton flowering stage accelerates phenology and declines the fiber quality of cotton. A two-year field trial was conducted to examine the effect of exogenous chitosan application in alleviating the effects of heat stress on seed cotton yield, quality, phenology, and glycine betaine synthesis. Three levels of heat treatments were assigned to the main plots. Five levels of foliar spray of chitosan, i.e., 0, 0.2, 0.4, 0.6, and 0.8 g L⁻¹, were applied in each subplot during heat stress imposition. The treatment plan was comprised of H₀ (control, no heat stress), H₁ (heat stress at flowering for 4 days), and H₂ (heat stress at flowering for 8 days). Heat stress at flowering for 8 days resulted in a remarkable decrease in glycine betaine synthesis, phenological parameters, seed cotton yield, and quality attributes compared to the control. The effects of heat stress were more pronounced when the exposure time was 8 days compared to 4 days. Chitosan foliar application significantly improved glycine betaine, seed cotton yield, earliness of maturity, and fiber quality, decreasing malondialdehyde contents in heat-stressed cotton. In contrast, the premier dose (0.8 g L⁻¹) of chitosan proved more efficient than lower doses. It is concluded that exogenous application of chitosan at 0.8 g L⁻¹ was beneficial to arbitrating heat stress effect owing to its positive effect on fiber quality and seed cotton yield (increased by 22% over control).