As a common post-translational modification pathway, glycosylation plays important roles in maintaining proteins’ inherent conformations and normal functions. The contribution of core N-glycans formed in endoplasmic reticulum (ER) to plant tolerance against salt stress has been well-studied; however, the knowledge about the involvement of complex N-glycans synthesized in Golgi apparatus is limited. Here, we report that a pepper N-acetylglucosaminyl-transferase III gene CaGnT-III, which takes part in the maturation of complex N-glycans, can respond to heat, salt, and drought stress. Furthermore, silencing of CaGnT-III compromises pepper tolerance and its overexpression enhances Arabidopsis tolerance, to the above abiotic stresses. Under stressed conditions, compared to those in the control with empty vector, in CaGnT-III silenced pepper seedlings, the increase of MDA (malondialdehyde) accumulation and the decrease of total chlorophyll content were aggravated, while the enhancement of proline content, CAT (catalase) and APX (ascorbate peroxidase) activities, and stress-related genes expression were weakened. On the contrary, overexpression of CaGnT-III in Arabidopsis presented the opposite results. Therefore, we speculate that CaGnT-III gene positively regulates the formation of plants tolerance to abiotic stress by enhancing antioxidant ability.