Geological CO2 sequestration (GCS) can help mitigate global warming and enhance methane recovery from coal beds. However, few studies have linked the effects of CO2 to surface chemistry changes controlling wetting behavior in deep coal beds. Contact angles (CAs) of CO2/N2-high volatile bituminous coal-water systems were measured under different temperatures and pressures. The surface chemistry and physical structure of coals were characterized to investigate changes in physicochemical properties and their relations with wettability after reactions. For N2 treatment, the time-dependence of static and dynamic CAs were insignificant, ranging within 4°. For gaseous CO2 treatment, the static CAs and the average advancing angles increased slightly. With supercritical (sc) CO2, both the static and dynamic CAs increased significantly, and θadv changed to intermediate-wet (92°). Reactions with minerals exposed to scCO2 resulted in greater surface roughness and heterogeneity, greater contact angle hysteresis and more surface sites occupied by scCO2 rather than H2O. Increases in hydrophobic functional groups and decreases in hydrophilicity were shown by FTIR spectra, reflecting the shedding of polar oxygen-containing functional groups, reduction of hydrogen bonds, and increasing percentage of hydrocarbons. XRD patterns obtained following scCO2-treatment showed that crystallite growth and molecular polymerization were higher toward graphite-like. The calculated structural parameters of functional groups and crystallites both showed elevated coal rank. Changes in crystallite structure, notably higher carbon content and decreased negative surface charge, are unfavorable for water-wetting. This study contributes to understanding surface chemistry changes responsible for decreased wettability during CO2-enhanced coal bed methane recovery and GCS in coal reservoirs.