This work discussed the origins, alteration and accumulation processes of the oil and gas in the Kekeya gas condensate field based on molecular compositions, stable carbon isotopes, light hydrocarbons, diamondoid hydrocarbons and biomarker fingerprints. A comparison study is also made between the geochemical characteristics of the Kekeya hydrocarbons and typical marine and terrigenous hydrocarbons of the Tarim Basin. Natural gas from the Kekeya gas condensate field is derived from Middle–Lower Jurassic coal measures while the condensates are derived from Carboniferous–Permian marine source rocks with a higher maturity. In the study area, both natural gas and condensates have experienced severe water washing. A large amount of methane was dissolved into the water, resulting in a decrease in the dryness coefficient. Water washing also makes the carbon isotopic compositions of the natural gas more negative and partially reverse. Considering that the gas maturities are higher than once expected, gas generation intensity in the study area should be much stronger and the gas related to the Jurassic coal measures could promise a greater prospecting potential. As a result of evaporative fractionation, the Kekeya condensates are enriched in saturates and lack aromatics. Evaporative fractionation disguises the original terrigenous characteristics of the light hydrocarbons associated with the natural gas, making it appear marine-sourced. Thus, alteration processes should be fully taken into consideration when gas–source correlations are carried out based on light hydrocarbons. With the condensates discovered in the study area all being “migration phase”, the pre-salt Cretaceous and Jurassic reservoirs may promise great exploration potential for the “residual phase” hydrocarbons. This research not only is of significance for oil and gas exploration in the southwest Tarim Basin, but also sheds light on the oil/gas-source correlations in general.