Fluoride-based plasma treatment is a robust technique that enables shallow implantation of fluorine ions into group III-nitride epitaxial structures. This technique has been used to achieve robust threshold voltage control of the AlGaN/GaN high electron mobility transistors and led to the realization of self-aligned enhancement-mode devices. To reveal the atomic scale interactions and provide a modeling tool for process design and optimization, a molecular dynamics (MD) simulation is conducted for fluorine plasma ion implantation. Specific potential functions are applied to calculate the interactions among atoms and simulate the dynamic process of fluorine ions’ penetration and stopping in III-nitride materials. The MD simulation provides accurate information on dopant profiles that are verified by secondary-ion-mass-spectrum measurements. Defect formation and distributions, that are critical in process development, are also investigated.