Affibody‐conjugated RALA (affi‐RA) are designed for delivering oligomeric 5‐fluorodeoxyuridine (FUdR, metabolite of 5‐FU) strand to raise the selectivity of 5‐fluorouracil (5‐FU), decrease its toxicity and improve its suboptimal therapeutic efficacy. The nanodrugs, FUdR@affi‐RA, are spontaneously assembled by electrostatic interaction between positively charged affi‐RA and negatively charged FUdR15‐strands (15 consecutive FUdR). FUdR@affi‐RA exhibits excellent stability under simulated physiological conditions. Compared with free FUdR, FUdR@affi‐RA shows excellent targeting and higher cytotoxicity in human epidermal growth factor receptor 2 (HER2) overexpressing gastric cancer N87 cells. Moreover, the anticancer mechanism studies reveal that FUdR@affi‐RA enhances the expression and activity of apoptosis‐associated proteins in the Bcl‐2/Bax‐caspase 8,9‐caspase 3 apoptotic pathway induced by FUdR. This study indicates that the fusion vector, affi‐RA, presents a promising delivery system platform for nucleoside analogue drugs and provides a new strategy for the development of therapeutics of cancer treatment.