5,8-Hihydroxyl-1,4-naphthazarin was taken as a model compound to explore the effect of halogen substitution on intramolecular proton transfer process. Calculations indicate that the substitution in the R2- and R4-positions far away from the active region has much weaker influence on the IPT process than that in the R1- and R3-positions. IPT barriers for substitution in the R1-position are higher than that of parent molecule. However, it is quite reverse for substitution in the R3-position. The IPT process is a proton transfer process coupled with charge separation and coulombic interaction would be dominant during this process. As for naphthazarin, halogen substitution would decrease the quantum yields of O2 but increase those of 1O2.