Penglai sea cucumber (Apostichopus sp.) is a newly developed aquaculture species. The nutrient composition in the body wall of Penglai sea cucumber has not been investigated widely. The current study measured the nutrient composition of Penglai sea cucumber and compared with other sea cucumber species. Results showed that the contents of moisture, crude protein, crude fat, and crude ash of the body walls of Penglai sea cucumber were 91.29%, 5.25%, 0.23% and 3.09%, respectively, The contents of crude protein and crude ash were higher than those of Apostichopus japonicus, whereas the contents of moisture and crude fat were lower than those of A. japonicus. The total amino acids (TAA) content of Penglai sea cucumber was 53.76%, which was significantly higher than that of A. japonicus. Furthermore, the flavor amino acids (FAA) content was 25.63%, which accounted for 47.66% of TAA. The FAA contents were higher than those of A. japonicus, suggesting that Penglai sea cucumber might be more delicious than other sea cucumber species. In addition, the contents of PUFA and “DHA+EPA” were 26.47% and 12.08%, respectively and the UFA/SFA ratio was 3.19 in Penglai sea cucumber, which were higher than those in A. japonicus. The body wall of Penglai sea cucumber has great content in major and trace element, VB6, VB1, and suitable Ca/P ratio. The content of VB1 was 1.3 mg/100 g, which was higher than that of A. japonicus. In conclusion, Penglai sea cucumber bears better nutrition condition, and is a promising species for aquaculture and stock enhancement.