Halogen monolayer on a silicon surface is attracting active attention for applications in electronic device fabrication with individual impurities. To create a halogen mask for the impurities incorporation, it is desirable to be able to remove a single halogen atom from the surface. We report the desorption of individual halogen atoms from the Si(100)-2×1-Cl and -Br surfaces in a scanning tunneling microscope (STM). Silicon dangling bonds (DBs) formed on the Si surface after halogen desorption were investigated using STM and the density functional theory. Three charge states: positive, neutral, and negative were identified. Our results show that the charge states of DBs can be manipulated, which will allow to locally tune the reactivity of the Cl-and Br-terminated Si(100) surfaces.