Purpose The incidence and mortality of secondary malignant tumors (MT) in people living with HIV(PLWH) are increasing. The purpose of this study is to analyze the characteristics of Complete Blood Count (CBC), bone marrow and immunity in PLWH with secondary MT, so as to provide data reference for diagnosis and risk factor assessment strategies of such patients.Methods We collected 297 patients who were diagnosed with PLWH and required bone marrow examination, including 101 cases of PLWH with secondary MT and 196 cases of PLWH without MT. The CBC, bone marrow and immune index of the two groups of patients were retrospectively analyzed.Results In terms of WBC, RBC, HGB, PLT, NEUT, the granulocyte ratio in bone marrow and CD4 cell counts, both were lower than those of pure PLWH. The independent risk factors of PLWH with secondary MT were HGB < 90g/L (RR = 1.581, 95%CI: 1.030–2.427, P = 0.036), the morphology of RBC in BM showed senescent nuclei and immature cytoplasm (RR = 1.489, 95%CI: 1.006–2.203, P = 0.046) and CD4 cell count < 100 cells/ul (RR = 2.307, 95%CI: 1.406–3.787, P = 0.001). HGB < 60g/L and RBC ratio of bone marrow < 0.2 were the independent risk factors associated with prognosis. The best hematologic predictor of PLWH with secondary MT was HGB (AUC = 0.707, 95%CI: 0.642–0.772, P < 0.001).Conclusion Severe anemia, the abnormal morphology of RBC in bone marrow, severe immune deficiency increase the risk of secondary MT in PLWH. Severe anemia and decreased RBC ratio in bone marrow are independent factors affecting the prognosis of PLWH with secondary MT.