In this study, novel silicon(iv) phthalocyanines axially disubstituted with bis[(4-{3-[3-(dimethylamino)phenoxy]propoxy}phenyl)methoxy] and bis[(4-{3-[3-(diethylamino)phenoxy]propoxy}phenyl)methoxy] groups and their quaternized derivatives were synthesized and characterized. Then, their supercoiled pBR322 plasmid DNA cleavage properties were investigated using agarose gel electrophoresis. The in vitro PDT effects of Si-3a and Si-4a were investigated using the MTT cell viability assay against HCT-116, A549 and SH-SY5Y cell lines. Si-3a and Si-4a did not show cleavage effects upon increasing concentrations in the dark but both compounds showed cleavage activities upon irradiation for 30 and 60 min, respectively. The MTT cell viability assay indicated that Si-4a had a cytotoxic effect in a concentration-dependent manner on the HCT-116 cell line but it did not show any statistical difference with regard to phototoxicity. Otherwise, Si-3a and Si-4a had significant phototoxic effects when compared to cytotoxic effects against A549 and SH-SY5Y. The results suggested that Si-3a and Si-4a showed better cell death against SH-SY5Y than other cell lines with irradiation.