The large Stokes shifts usually result in open circuit voltage (VOC) reduction, which will affect the photovoltaic performance of the material. Recently, three-dimensional organosulfide-halide perovskites (CYS)PbCl2 and (CYS)PbBr2 [CYS: +NH3(CH2)2S−] have received much attention in the photovoltaic field due to their higher stability and similar photoelectric properties (desirable direct bandgap, band dispersion, and light absorption) than MAPbX3 (X = Cl, Br, and I). Unfortunately, both materials exhibit large Stokes shifts emission. Thus, to be clear about their application prospects in the photovoltaic field, the origin of the large Stoke shift needs to be investigated. Moreover, the bandgaps of (CYS)PbBr2 (2.17 eV) and (CYS)PbCl2 (2.32 eV) are higher than the ideal bandgap value of (0.9–1.6 eV) for photovoltaic materials. Based on density functional theory, this paper explores the cause of large Stokes shifts and further improves the photovoltaic performance of the materials by halogen substitution. The calculation results show that the large Stokes shifts come from defect emission rather than intrinsic self-trapping emission and the I atom substitution can reduce the bandgap [(CYS)PbI2; gap = 1.85 eV] and enhance the optical absorption and carrier migration ability without destroying the direct bandgap. Our research will promote the experimental synthesis of more excellent perovskite photovoltaic materials.