Current plasma cleaning technologies have been proven effective in removing organic contaminants from the surfaces of optical components; however, they still suffer from low cleaning efficiency and an uncontrollable cleaning process. The fundamental reason for these shortcomings lies in the lack of a profound understanding of the microscopic mechanisms by which plasma removes organic contaminants. Therefore, this study proposed using reactive molecular dynamics simulations to elucidate the microscopic physicochemical mechanisms through which energetic reactive species in plasma degrade organic contaminants. This research aims to investigate the microscopic reaction processes and the factors influencing plasma's cleaning efficiency in removing organic contaminants. Firstly, a physicochemical interaction model was constructed based on reactive force fields to describe the interactions between typical reactive oxygen species in plasma and representative organic contaminants in a vacuum system. The molecular-scale dynamics of bond breaking and reconfiguration, reaction products, and the mechanism of layer-by-layer removal during the plasma degradation of organic contaminants are described over picosecond timescales. Secondly, the study systematically discusses the effects of key cleaning parameters, such as plasma energy, plasma flux, and environmental temperature, on the removal efficiency of organic contaminants during plasma cleaning. The findings provide a theoretical foundation and technical support for enhancing the efficiency of plasma cleaning for organic contaminants on the surfaces of optical components and for controlling the cleaning process.