We synthesized three chelate‐tethered purine ligands, having a Schiff base linkage at the N9 position, which resulted in the dipolar imine‐methoxyphenol adenine Schiff base HL1, the 2‐aminopurine Schiff base HL2, and the 2,6‐diaminopurine Schiff base HL3. These ligands selectively showed enhancement of the fluorescence of the zinc ions. The imine‐based compound HL1 chelated with zinc ions to give the discrete dimeric structure 1, a green fluorescent complex, which was again stabilized by purine–purine interactions to give a 1D polymeric structure. The ligands having a 6‐amino group, HL1 and HL3, have high quantum yield, which gives higher fluorescence enhancement of the free zinc ions in the HeLa cells. HL1 was localized in the cytoplasm and the nucleoli of the HeLa cells, which was confirmed by an RNase digestion test.