The purpose of this investigation was to determine the characteristics of the clinical manifestations, laboratory findings and prognostic impact of the thrombocytopenia patients with systemic lupus erythematosus (SLE). The case group of 47 SLE patients with thrombocytopenia and the control of 49 SLE patients with normal platelet number were reviewed retrospectively. The clinical manifestations, immunological profiles, hemograms and myelograms, disease activity (SLEDAI-2K), end organ damages (SLICC) and survival rate at the time of follow-up were recorded. The analysis of clinical manifestations showed that the case group was more likely to be with renal disease (p = 0.038), and less skin rash (p = 0.032). The analysis of the hemograms revealed that the case group was more concomitant with anemia, leucopenia and neutropenia than the control group (p < 0.001, p = 0.014 and p = 0.02, respectively). Moreover, it was also revealed that the SLE patients with thrombocytopenia were often in the condition of higher disease activity, had more probability of end organ damage, and were associated with a higher mortality rate (P = 0.041, p = 0.035 and p = 0.038, respectively). The clinical data and laboratory findings were different between the SLE patients with thrombocytopenia and those with normal platelet number. Thrombocytopenia can be recognized as a reliable prognostic marker to identify a subset of patients with higher disease activity, more possibility of end organ damage and higher mortality.