Genetically engineered T cell therapy is emerging as a potent strategy for treating hematological and solid malignancies. Although lentivirus is the most common vector for T cell gene modification, its transduction efficacy remains unsatisfied especially during the manufacturing process. Herein, glycometabolic bioorthogonal chemistry is utilized to establish a highly efficient viral transduction system for human primary T lymphocytes. Azide motifs are anchored on the T cell surface via the intrinsic glycometabolism of exogenous azide–glucose, serving as an artificial ligand for viral binding. The complementary functional moiety dibenzocyclooctyl (DBCO)-conjugated PEI (PEI-DBCO) is then coated on lentiviral surface, which strengthens the virus–T cell interaction through DBCO/azide bioorthogonal chemistry. The results show that the PEI-DBCO/azide–glucose system effectively facilitates viral binding to T cells and elevates the transduction efficiency of the lentivirus from 20% to 80% without any effect on T cell proliferation and activity. More importantly, the PEI-DBCO/azide–glucose system significantly doubles the yield of anti-CD19 chimeric antigen receptor T (CAR-T) cells and robustly boosts their antitumor capability compared to polybrene-assisted lentiviral transduction both in vitro and in vivo. Overall, the bioorthogonal PEI-DBCO/azide–glucose system significantly boosts viral transduction efficacy and exhibits a powerful gene-manipulating capability in human primary T cells, thereby showing a great potential for clinical-engineered T lymphocytes manufacture.