In the present study, the biochemical compositional differences in the hard and soft shell of blue swimming crab (Portunus pelagicus) were examined. Proximate composition, protein fractions, minerals, amino acids and fatty acids, are the parameter analyzed along with FTIR spectral analysis to find out functional group variation. The average moisture, protein, fat & ash content of hard shell crabs was 79.02±3.08%, 13.64±1.40%, 0.79±0.57% and 2.55±0.27% and that of soft shell crabs was 83.78±1.02%, 9.34±0.85%, 0.34±0.26% and 3.46±0.58%. Significant difference was observed in protein (p < 0.05), but not in fat and ash contents (p > 0.05). Sarcoplasmic proteins are the major fraction (43-45%) followed by myofibrillar protein (25-30%) and alkali soluble proteins (24-25%). No significant differences in the protein fraction among the crabs (p > 0.05). The six major minerals viz: Mg, Ca, Mn, Fe, Cu, and Zn were recorded in crab showing an average conc. of 21 ppm. There was a significant difference in Zn concentration among the soft and hard shell crabs (p < 0.05). Saturated, monounsaturated and polyunsaturated fatty acids were 56.35%, 11.61% and 9.69% in hard shell crabs and 50.43% and 3.49%, 12.35% in soft shell crabs, respectively. This study showed that hard shell crab have more nutritional value in terms of proteins, mineral and health beneficially PUFA.