This dataset includes organic content and amino acid δ15N data of Site MD10-3340 and grazing proportion calculation. Site MD10-3340 (00°30.98′S, 128°43.47′E) locates at the Halmahera Sea in the western equatorial Pacific at a water depth of 1094 m, recovered with a giant piston corer during the MD181 MONOCIR cruise in 2010. The uppermost 17 m of this core were analyzed, covering the last 140 ka. Organic carbon and organic nitrogen content of the sediments were measured after removing carbonates and clay minerals, using 72 samples from this site. Fifty-one samples from this site were used for amino acids δ15N analyses, which includes pretreatment with acid hydrolyzation, purification, and derivatization, following measurement with GC-IRMS. The concentration and δ15N are obtained for 4-9 individual amino acids in each sample, including: glycine (Gly), valine (Val), serine (Ser), threonine (Thr), asparagine (Asp), glutamic acid (Glu), phenylalanine (Phe), lysine (Lys), and tyrosine (Tyr). To quantitatively reflect changes in trophic structure, the grazing proportion is calculated using amino acids δ15N of phenylalanine and glutamic acid, following the setting of an idealized ecosystem model. All pretreatments and measurements in this study are conducted at Tongji University in Shanghai.