Red/near-infrared organic dyes are becoming increasingly widespread in biological applications. However, designing these dyes with long-wavelength emission, large Stokes shifts, and high fluorescence quantum efficiency is still a very challenging task. In this work, five donor-acceptor (D-A) red/near-infrared fluorophores based on different chlorinated/fluorinated benzo[c][1,2,5]thiadiazole units are designed and synthesized. The photophysical, theoretical calculations, and electrochemical properties explored in this study have proved that the introducing of chlorine atoms will lead to a lower HOMO level, stronger steric hindrance, and a relatively lower quantum yield in solutions. When the organic dots are fabricated, the chlorinated dots demonstrate much higher fluorescence quantum yield, larger Stokes shift, and better photostability than that of the fluorinated dots. After labeling A549 cells, all the chlorinated/fluorinated dots exhibit high red emission intensities. All these results indicated that the subtle change in the halogen atom of the benzo[c][1,2,5]thiadiazole unit is a unique method to tune the photophysical properties of those materials, and also provides good guidelines to design highly efficient red/near-infrared molecules for cellular imaging applications.