A novel fluorescent probe on the basis of Schiff base ((E)-4-((2-(8,9-di(naphthalen-1-yl)-9H- purin-6-yl) hydrazineylidene) methyl)-2-methoxyphenol named as PHM) for detecting Cu2+ and Pd2+ ions were designed and structurally described using biological purine scaffolds. This fluorescent probe can quickly recognize palladium and copper ions in the HEPES buffer solution system without interference from the rest of the metal ions. It’s detection limits in HEPES buffer solution for Cu2+ and Pd2+ ions were 72.97 nmol/L and 839 nmol/L, respectively. Meanwhile, naked eyes can detect a visual hue change, which could be due to its complexation with Cu2+ and Pd2+ ions, generated in the inhibition of photo-induced electron transfer effects. The fluorescence of PHM-Cu2+ was restored after the addition of EDTA, confirming the reversible property of PHM. A density flooding theory (DFT) and Job’s plot analysis backed up the binding processes of the fluorescence probe towards Pd2+ and Cu2+ ions.