Due to the tendency of refrigerated sword prawn (Parapenaeopsis hardwickii) to spoil quickly, affecting both muscle quality and microbial community characteristics in the shrimp heads, intact and headless sword prawn were used as the research object. To explore relevant changes, muscle physicochemical indexes and high-throughput sequencing results of two shrimp types were assessed after 0, 2, 4, and 6 d of chilled storage at 0 ℃. The results showed that the moisture content, water activity, L* values, and a* values in the muscle of both groups significantly decreased (P<0.05), while b* values increased (P<0.05) with the extension of chilled storage. The muscle fibers of fresh shrimp were closely and orderly arranged, while the gaps between myofibrils increased after chilled storage, as indicated by hematoxylin and eosin (H&E) staining and transmission electron microscopy. During chilled storage, the moisture content, water activity, and L*, a*, and b* values of headless shrimp were higher than those of intact shrimp, and the degree of myofibrillar fiber damage was lower. The microbial richness and diversity in shrimp muscle was the highest at the early stage of storage and diminished gradually. Proteobacteria were dominant at the phylum level (89.23%~99.82%). Delftia, Pseudoalteromonas, and Psychrobacter were dominant in the early and late stages of chilled storage at the genus level, respectively. The β diversity analysis revealed that two first principal coordinates accounted for 89.36% of the variance, and the bacteria community composition in headless shrimp after 2 d of chilled storage significantly differed from that in the other sample groups. In conclusion, head removal before sword prawn storage can effectively reduce the rate of muscle deterioration and microbial richness. These findings provide a theoretical basis for clarifying the changes in the muscle quality of sword prawn.