This paper reported a comparative analysis of nutritional value and structural characteristics between Apostichopus japonicas and Acaudina molpadioides with the aim of providing basic data for the deep processing of Acaudina molpadioides captured in Zhoushan sea area. The results showed that the crude protein content of Acaudina molpadioideswas 53.28%， and lower than Apostichopus japonicas. The protein of Acaudina molpadioides was mainly collagen and has a typical feature of collagen with α chain and β chain （98 ku and 102 ku in molecular weight， respectively）. The AAS of Acaudina molpadioides was lower than Apostichopus japonicas， and the first limited amino acid was lysine； There were many vitamins in Acaudina molpadioides， and most vitamins were lower than Apostichopus japonicas except VE（2.18 mg/100 g）； The Fe content of Acaudina molpadioides（150 mg/kg） was extremely higher than Apostichopus japonicas （2.3 mg/kg）， while the content of Pb and As was comparatively low. There were 23 fat acids in Acaudina molpadioides， among which were mainly MUFA（35.06%） and PUFA（30.86%）； SEM observations indicated that the muscle fibers of Acaudina molpadioides were thicker and packed in a messy and arrangement. It was very likely the main reasons for the great hardness of Acaudina molpadioides.