Blood stasis syndrome (BSS) is an important pathological condition in traditional East Asian medicine and is associated with ischemic heart disease, cerebral vascular accident, diabetes mellitus, chronic renal failure, severe traumatic injury, and dysmenorrhea. However, previous studies have been unable to reveal the clinical and biological characteristics or biological markers of BSS. We hypothesized that the heterogeneity among the manifestations of BSS or non-BSS could interfere with an analysis to describe the characteristics of BSS. In this study, male participants based on the severity of BSS-associated symptoms and signs were clustered and classified into four subgroups: BSS subgroups (1), (2), (3), and (4). Non-BSS core subgroup was redefined using manifestation cluster analysis. Biological characteristics of subgroups BSS(1) and BSS(2) belong to the range of the non-BSS core subgroup (1), whereas that of subgroups BSS(3) and BSS(4) are characterized by different biological parameters such as systemic inflammatory conditions and elevated D-dimer level. Our results suggested that patients in subgroups of BSS(3) and BSS(4) are more likely to be exposed in an inflammatory state than other BSS subgroups. We found the heterogeneity among the manifestations which could mask the characteristics of BSS and identified the clinical and biological profiles of the four BSS subgroups through comparisons of the redefined non-BSS and BSS subgroups. This finding could provide accurate diagnostic criteria and new approaches for BSS treatments in different subgroups.