Photodynamic therapy (PDT) has emerged as a new antitumor modality. Hypoxia, a vital characteristic of solid tumors, can be explored to stimulate the fluorescence response of photosensitizers (PSs). Considering the characteristics of PDT, the targeting of organelles employing PS would enhance antitumor effects. A new multifunctional cyanine-based PS (CLN) comprising morpholine and nitrobenzene groups was prepared and characterized. It generated fluorescence in the near-infrared (NIR) region in the presence of sodium dithionite (Na2S2O4) and nitroreductase (NTR). The response mechanism of CLN was well investigated, thus revealing that its obtained reduction product was CLNH. The obtained fluorescence and singlet oxygen quantum yield of CLNH were 8.65% and 1.60%, respectively. Additionally, the selective experiment for substrates indicated that CLN exhibited a selective response to NTR. Thus, CLN fluorescence could be selectively switched on and its fluorescence intensity increased, following a prolonged stay in hypoxic cells. Furthermore, fluorescence colocalization demonstrated that CLN could effectively target lysosomes. CLN could generate reactive oxygen species and kill tumor cells (IC50 for 4T1 cells was 7.4 ÎźM under a hypoxic condition), following its response to NTR. NIR imaging and targeted PDT were finally applied in vivo.