Petroleum engineers are always in a race to maximize the recovery factor out of naturally trapped hydrocarbon resources. Unconventional resources such as organic-rich shales have unlocked significant reserves attributed to the novel production technologies of lateral drilling assisted by hydraulic fracturing. Even though such techniques have enabled the exploitation of shales, the ultimate recovery remained fractional, a challenge to be answered through further improvement. Carbon dioxide injection in unconventional resources, which was initially implemented for coalbed methane, has been recently an active area of investigation for organic-rich shales. In this paper, we present a molecular modeling study of carbon dioxide injection in the organic matter of the shale matrix. We built the molecular model, consistent with the repeated organic matter characterization in the literature. Molecular dynamics (MD) protocol was developed to form a three-dimensional (3-D) configuration of kerogen, followed by Gibbs Monte Carlo simulation for the adsorption/desorption calculations, and self-diffusivity calculations through MD. The aim was to delineate the impact of carbon dioxide injection on the adsorption/desorption behavior coupled with its influence on the transport. Injection of carbon dioxide was found to shift the adsorption isotherm favoring the depletion of methane. The ultimate recovery raised from 54% (no injection of CO2) up to 92% depending on the carbon dioxide concentration and its temperature. Moreover, the injection of carbon dioxide was found to have a minimal impact on the self-diffusivity of methane in kerogen bodies and their associated microcracks.