The Saltpond Basin, situated within the South Atlantic margin of Ghana, is a significant area for petroleum exploration but has received relatively limited research attention. Previous studies have examined source rock composition, but data on crude oil organic chemistry are lacking, hindering understanding of the basin’s petroleum system and evolution. To address this gap, we analyzed biomarkers and stable carbon-isotope ratios in Saltpond Basin crude oil using gas chromatography–mass spectrometry and gas chromatography–isotope ratio mass spectrometry to elucidate organic matter source, depositional environment, and thermal maturity. Findings were compared with oils from the West African segment of the South Atlantic margin, namely the Tano Basin and the Niger Delta Basin, to identify potential correlations and gain insights into regional variations. Molecular and isotopic results unveiled a significant prevalence of organic matter derived from lower marine organisms. Patterns of organic matter deposition and preservation in Saltpond oil samples suggested a suboxic marine transitional environment, contradicting conventional understanding of terrestrial dominance in such settings. Moreover, the potential for degradation processes to obscure differentiation between terrestrial and marine organic matter origins underscores the complex nature of organic matter dynamics in transitional marine environments. Analysis of molecular thermal maturity indices suggested Saltpond oils were expelled from source rocks exhibiting thermal maturity at the early maturity stage. Correlation analysis unveiled genetic disparities among crude oils sourced from the Saltpond Basin and those from the Tano and Niger Delta Basin, primarily due to variations in source input and depositional environment conditions. Saltpond oil exhibits lower terrestrial organic input than Tano Basin’s crude oils, which also have less terrestrial input than Niger Delta Basin crude oils. Additionally, its paleodepositional environment notably differs from oils in the Tano Basin (anoxic transitional marine-lacustrine settings) and the Niger Delta Basin (suboxic–oxic terrigenous deltaic or marine or lacustrine environments). Thermal maturity range of Saltpond oil is comparable to oils in the Tano Basin but lower than oils in the Niger Delta Basin. These findings provide valuable insights into petroleum generation history and unique organic geochemical characteristics within the Saltpond Basin, essential for exploration, production, and environmental management efforts in the region. Furthermore, correlation studies provide evidence that distinct biological, geological, and paleoenvironmental conditions shaped various oil types in the West African segment of the South Atlantic margin.