•The two-photon (TP) photosensitizers (PS) of maximum absorption at 808 nm and maximum fluorescence at 660 nm can be potential for deep-seated tumor imaging and therapy.•The boron dipyrromethene (BDP) structure used in TP photodynamic therapy (PDT) possess favorable photophysical property (i.e., high molar extinction coefficients, superior fluorescent quantum yields, outstanding photo stability), and the indo-BDP in meso-position can efficiently improve the singlet oxygen quantum yield (0.39).•The cationic group in TP PS can efficiently improve the PDT efficacy (IC50=25.5 nM) compared with two neutral contrastive molecules (PG-Car-BDP and C10-Car-BDP).•The cationic PS TP-Car-BDP can efficiently target to tumor in vivo due to the structure inherent targeting. Two-photon (TP) have been innovatively researched in bio-imaging and photodynamic therapy (PDT) due to the near-infread (NIR) absorption and excellent spatial accuracy, especially for the subcutaneous and deep-seated tumor. For TP excited photosensitizers (PS), the NIR absorption and enough triplet state energy can be simultaneously realized by semi-excited mode. Thus, we reported a boron dipyrromethene based cationic two-photon photosensitizer (TP-Car-BDP) to promote the tumor targeting and optical physical properties for better imaging and therapeutic effect, using two neutral molecules (PG-Car-BDP, C10-Car-BDP) as comparison. As expected, the cationic group could accelerate oil-water balance and cellular uptake, realize structure-inherent targeting in vivo, and induced early apoptosis in PDT. The imaging and therapeutic property of TP-Car-BDP excited by one/two-photon was also compared to illustrate efficacy of TP. Moreover, the high singlet oxygen quantum yield (0.39) and excellent phototoxicity (IC50 of 25.5 nM, MB was 2960 nM) revealed the potential therapeutic capacity.