A number of cold seeps have been discovered in the northern South China Sea (SCS) including the Haiyang 4 cold-seep area where Core 973-5 was collected. Intact polar lipids (IPLs) and core lipids (CLs) were analyzed separately in sediments from Core 973-5. The most abundant lipid biomarkers were isoprenoidal GDGTs (isoGDGTs), with Crenarchaeol and GDGT-0 predominating. IPL-isoGDGTs and CL-isoGDGTs were mainly derived from Thaumarchaeota. IPL-isoGDGTs were mainly produced and retained in situ thus containing most of the in situ microbiological information. Branched GDGTs were predominantly derived from generated in marine production, and mixed with some terrestrial inputs. All IPLs groups presented a high value in the sulfate-methane transition zone (SMTZ). Furthermore, IPL and CL-MI, IPL-R0/4 showed the highest values within the SMTZ, while IPL and CL-R4/i had the lowest values at the SMTZ, suggesting that the contribution of Methanophila and methanogenic to GDGTs increased, while the contribution of ammonia-oxidizing Archaea to GDGTs decreased at the SMTZ.