Thrombosis is a major cause of morbimortality in patients with polycythemia vera (PV). Furthermore, neutrophils play a significant role in thrombosis, but their role in the pathogenetic mechanisms of PV is not well characterized. Therefore, we investigated the role and mechanisms by which neutrophils regulate thrombosis in PV patients. Univariate and multivariate logistic regression analysis of clinicopathological factors was performed to determine the independent risk factors of thrombosis in PV. Pearson's correlation analysis was performed to determine the relationship between absolute neutrophil count (ANC) and the hypercoagulable state in PV patients. Bioinformatics analysis of the GSE54644 dataset was used to identify hemostasis-related pathways in neutrophils of PV patients. Weighted gene co-expression network analysis (WGCNA) of the integrated dataset (GSE57793, GSE26049 and GSE61629) was used to identify neutrophils-related genes and pathways associated with thrombosis in PV. Ingenuity pathway analysis (IPA) was performed to identify the differentially activated pathways in PV patients with or without thrombosis using GSE47018 dataset. Our data showed increased ANC in PV patients. Multivariate logistic regression analysis showed that ANC was an independent risk factor for the thrombotic events in PV patients before or at diagnosis. ANC correlated with the hypercoagulable state in PV patients. Neutrophil extracellular traps (NETs) pathway was significantly enriched in the neutrophils of PV patients. IPA results demonstrated that PRKCD-mediated NETs pathway was hyperactivated in PV patients with thrombosis. In summary, ANC was an independent risk factor for the thrombotic events in PV patients before or at diagnosis, and PRKCD-mediated NETs pathway was aberrantly activated in the neutrophils of PV patients and was associated with the thrombotic events.