An ab initio approach with the density functional theory (DFT) method was used to study F atom interactions with organosilicate glass (OSG)-based low-k dielectric films. Because of the complexity and significant modifications of the OSG surface structure during the interaction with radicals and etching, a variety of reactions between the surface groups and thermal F atoms can happen. For OSG film etching and damage, we propose a multi-step mechanism based on DFT static and dynamic simulations, which is consistent with the previously reported experimental observations. The important part of the proposed mechanism is the formation of pentavalent Si atoms on the OSG surface due to a quasi-chemisorption of the incident F atoms. The revealed mechanism of F atom incorporation into the OSG matrix explains the experimentally observed phenomena of fast fluorination without significant modification of the chemical structure. We demonstrate that the pentavalent Si states induce the weakening of adjacent Si–O bonds and their breaking under F atom flux. The calculated results allow us to propose a set of elementary chemical reactions of successive removal of CH3 and CH2 groups and fluorinated SiOx matrix etching.