Light hydrocarbons (LHs) retain comprehensive information about the genesis of natural gas. In this study, the gas composition, carbon isotopes, and LHs in deep marine natural gases from the Tarim Basin were comprehensively analyzed, along with comparative data on oil-cracked dry gases in the Sichuan Basin, to evaluate the diagnostic potential of LHs for deep natural gas genesis. The results demonstrate that the deep natural gases in the Tarim Craton are predominantly of thermogenic origin, sourced from sapropelic organic matter within marine shales. The analyzed gases exhibit maturities ranging from mature to over-mature stages, generated through both primary kerogen cracking and secondary cracking of oil and wet gas. These deep natural gases display distinct LH signatures at different thermal cracking stages. Initial cracking leads to an enrichment of n-alkanes, while the severe cracking stage (wet gas cracking stage) results in a pronounced shift toward cyclo-alkanes and aromatics. LH indicators related to the organic matter type and source rock lithology remain reliable during the initial cracking stage but become distorted under the severe cracking stage. The K1 genetic comparison index and the 2,4-/2,3-dimethylpentane ratio retain diagnostic validity across all cracking stages, whereas other genetic comparisons and thermal maturity parameters are only applicable in the initial cracking stage. Additionally, ratios associated with biodegradation and evaporative fractionation are influenced by thermal cracking. Several ratios, such as methylcyclohexane/n-heptane, methylcyclohexane/cyclohexane, and (2- + 3-) methylhexane/n-hexane effectively differentiate primary cracking gases from severely cracked gases. The latter are characterized by elevated cyclo-alkane to n-alkane ratios of the C6 range and aromatic to aliphatic ratios of the C6–C7 range, suggesting their potential as novel proxies for cracking intensity. Furthermore, similar to the 2,4-/2,3-dimethylpentane ratio, the two ratios of 2,2-/2,3- and 3,3-/2,3-dimethylpentane exhibit a systematic increase with thermal maturity, indicating their promise as robust indicators of thermal stress.