Background Eosinophilic chronic rhinosinusitis with nasal polyps (ECRSwNP) is a distinct phenotype of chronic rhinosinusitis with nasal polyps (CRSwNP), with many significantly different clinical features from non-eosinophilic chronic rhinosinusitis with nasal polyps (non-ECRSwNP). Thus, identification of subtypes is crucial for precise treatment. Immunohistology is a reliable way to present the subtypes; however, the results mainly depend on the observation of pathologist, and the method with automatic readout and the corresponding biomarkers is lacking. Objective The purpose of our research was to explore the predictive value of quantitative reverse transcription polymerase chain reaction (qRT-PCR) as an alternative method and messenger RNA (mRNA) expression of Charcot-Leyden crystals (CLC) as a corresponding target for ECRSwNP, which may benefit the automatized judgment. Method CLC mRNA levels in tissue samples from 48 CRSwNP patients and 10 controls were evaluated by quantitative real-time PCR. Hematoxylin and eosin staining was performed for histological assessment of CRSwNP and subtyping as ECRSwNP and non-ECRSwNP. Factors associated with ECRSwNP were determined with logistic regression analysis, the predictive value was presented by a receiver operating characteristic (ROC) curve, and optimal cutoff points of the predictors were identified as the Youden index. Results mRNA level of CLC in ECRSwNP was significantly elevated compared to either non-ECRSwNP group or control group, with no significant difference between non-ECRSwNP patients and controls. CLC mRNA levels were positively correlated with percentages of tissue eosinophil and peripheral blood eosinophil (P < .001, r = .683; P = .003, r = .420, respectively). Logistic regression analysis revealed CLC mRNA level and blood eosinophil percentages were prediagnosis factors (P = .007, P = .045, respectively) for ECRSwNP. ROC curves analysis indicated the area under the curve (AUC) of CLC mRNA level was 0.948 which was superior to the blood eosinophil percentage (AUC = 0.797; P = .044) as an optimal biomarker to predict ECRSwNP. Conclusions CLC mRNA levels based on the qRT-PCR may serve as a reliable and alternative method for the identification of ECRSwNP.