The main aim of the present work was to investigate the effect of the inherent differences in the raw muscle on the textural quality of the cooked meat from different sized Eriocheir sinensis. The content of entrapped water was 73.8–77.7 g/100 g in raw muscle. The density and diameter of muscle thick microfilaments ranged between 137 and 158/μm2 and 20.9–27.0 nm. These results demonstrated that the raw muscle from the tender group had a smaller density of larger diameter thick microfilaments and more entrapped water than other samples, which could explain the high tenderness of the cooked meat (P < 0.05). The potential structural proteins that indicated tenderness include myosin regulatory light chain 2, ancient ubiquitous protein 1, tubulin α-2 chain, and β-catenin, was determined using liquid chromatography-tandem mass spectrometry. The inherent attributes of raw muscle could explain the textural differences of the cooked meat from Eriocheir sinensis.