Deep-sea sediments, like those in the Mariana Basin, hold various contaminants, including petroleum hydrocarbons. However, little is known about their distribution, potential risks, sources, and fate. This study analyzed 38 surface sediments and 3 sediment cores, finding ∑n-alkanes and ∑PAHs concentrations at 705.43 ± 22.93 and 37.73 ± 1.62 ng/g dw, respectively. Hydrocarbons posed minimal risks and likely originated from aquatic (n-alkanes) and pyrogenic (PAHs) sources. Microbial activity, especially in deeper layers, influenced hydrocarbon degradation, with the deepest layer showing the highest degradation potential, highlighting microbial roles in hydrocarbon transformation in deep-sea sediments. Overall, this work carries out the sources, hazards, and biological removal of hydrocarbons from deep-sea sediments and facilitates the exploration of the life cycle of organic pollutants in extreme environments.