Objective The correlation between the expression of KIF3B mRNA and the pathological characteristics of skin basal cell carcinoma. Methods Retrospective analysis of 72 specimens of BCC patients diagnosed by pathology and 20 specimens with normal skin tissue surgically removed from outpatient patients in our hospital from January 2023 to December 2024. Divide them into a case group and a control group, and the differences of KIF3B mRNA expression levels between the two groups were compared. Based on the pathological subtypes of the lesions, 72 BCC patients were classified into sclerosing basal cell carcinoma group (i.e. invasive basal cell carcinoma group, IBCCs) and nodular and superficial phenotype group (i.e. non-invasive basal cell carcinoma group, NIBCCs). The differences of KIF3B mRNA expression levels and pathological features between the two groups of patients were compared, and the correlation between KIF3B mRNA and its pathological features was analyzed, as well as its predictive power for BCC. Results The expression level of KIF3B mRNA in the case group was higher than that in the control group (P<0.05). The expression level of KIF3B mRNA in IBCCs group was higher than that in NIBCCs group (P<0.05). The proportion of lesions with diameter>1cm and the proportion of deep invasion in the IBCCs group were higher than those in the NIBCCs group (P<0.05). The expression level of KIF3B mRNA was positively correlated with the lesion diameter and the proportion of deep invasion in BCC patients (P<0.05). The sensitivity and specificity of KIF3B mRNA expression level in predicting BCC were 89.23% and 75.35%, respectively (AUC=0.866). Conclusion KIF3B mRNA is highly expressed in BCC patients, and its expression level is closely related to the pathological characteristics of BCC patients. Detection of KIF3B mRNA expression level can early identify the risk of BCC.