The pH-related fluorescence quenching mechanism of 2-amino-4-hydroxypteridine (pterin), a biologic functional molecule, in the presence of acetate ion has been fully investigated for the first time. Using a combined experimental and theoretical approach, we discover that the fluorescence quenching observed in acid condition originated from a barrierless excited-state proton-transfer process. The proton on the acid form of pterin is transferred to acetate after photoexcitation. The hydrogen-bonding patterns are found to change with the pH values that govern the occurrence of excited-state proton transfer (ESPT). As revealed by investigating the excitation and relaxation processes of pterin, this ESPT process shows impressive site specificity intrinsically due to the photoinduced acidic center shifting. The experimentally observed fluorescence quenching and lifetime shortening of pterin in acid condition are thus attributed to the site-specific proton transfer from the N5 site. Pterin exists extensively in living organisms and has been found to show favorable proton-donating ability, which may transfer its proton to biofunctional molecules with hydrogen-accepting groups and induce related bioeffects.