Objective To investigate the significance of lymphocyte structure parameters of Sysmex XN-9000 hematology analyzer in screening peripheral blood atypical lymphocytes when positive alarm of atypical lymphocytes occurs. Methods From Dec. 2017 to Dec. 2018, 370 blood samples with positive alarm of atypical lymphocytes, which were detected by XN-9000 hematology analyzer in outpatient and emergency department of Changhai Hospital, Naval Medical University (Second Military Medical University), were collected in this study. Six lymphocyte structure parameters were recorded, including lymphocyte complexity (L-X), lymphocyte fluorescence intensity (L-Y), lymphocyte size (L-Z), dispersion width of lymphocyte complexity (L-WX), dispersion width of lymphocyte fluorescence intensity (L-WY) and dispersion width of lymphocyte size (L-WZ). According to the atypical lymphocyte proportion detected manually under microscope, the 370 samples were divided into 2 groups:atypical lymphocyte positive group (100 samples with an atypical lymphocyte proportion>5%) and atypical lymphocyte negative group (270 samples with an atypical lymphocyte proportion ≤ 5%), and the significance of each lymphocyte structure parameter was evaluated by receiver operating characteristic (ROC) curve. Then the parameters with high accuracy for screening atypical lymphocytes were analyzed by logistic regression model to study the significance of their combination. Results The lymphocyte structure parameters L-WY, L-X and L-Z had high accuracies in screening atypical lymphocytes, with the ROC area under curve (AUC) being 0.927, 0.939 and 0.931, respectively. The combined predictor was generated using L-WY, L-X and L-Z by logistic regression analysis model, and the ROC AUC of combined predictor was 0.979. When 0.058 1 was selected as the cut-off value, the sensitivity was 100.0% and the specificity was 77.8%. Conclusion Lymphocyte structure parameters L-WY, L-X and L-Z detected by Sysmex XN-9000 hematology analyzer can effectively screen peripheral blood atypical lymphocytes when positive alarm of atypical lymphocytes occurs.