Petroleum fluids in the deep Ordovician reservoirs of the Tarim Basin vary in phase and molecular composition. An improved understanding of the secondary geochemical alteration processes is critical for successful exploration and fluid property prediction. Three oil samples from the Ordovician condensate and oil reservoirs were analyzed using comprehensive 2D gas chromatography/time-of-flight mass spectrometry (GCxGC-TOFMS). Molecular signatures revealed varying levels of diamondoids and organosulfur compounds (OSCs) that were preferentially enriched in the condensate and a gas saturated oil; however, these molecular signatures were not generated through in-reservoir oil cracking or thermochemical sulfate reduction (TSR) as favorable thermal and medium conditions were not available. Severe cracking and TSR occurred in deeper Cambrian source-reservoirs and generated secondary geochemical products including diamondoids, OSCs, and H2S. Such secondary products were carried by dry gases derived for oil cracking that migrated upward through the fault system and filled shallower Ordovician oil reservoirs. The differential secondary gas charge can account for the variable fluid composition and varying phase behavior, i.e. the transition from unsaturated oil to gas saturated oil and then to condensate. Condensates were formed from the dissolution of primary oils due to extra gas mixing.