Singlet oxygen is the key element for photodynamic therapy. In this paper, six novel distyryl-BODIPY compounds were synthesized and investigated in detail to fully evaluate their photophysical/chemistry characteristics. Specially, the singlet oxygen (O-1(2)) quantum yield of compounds 2 and 4 each bearing two bromine atoms in their skeleton revealed the position effect of heavy atom for O-1(2) production. The O-1(2) quantum yield of 4, which was brominated at 2/6 position of BODIPY skeleton, was much higher than that of compound 2, brominated at styryl group with a long distance toward BODIPY core. Importantly, theoretical calculations were carried out to elaborate the essential reason for the difference of 2 and 4 by investigating intersystem crossing rate.