Introduction To determine the prevalence, clinical outcomes, and factors associated with hydroxyurea (HU) resistance or intolerance among polycythemia vera (PV) and essential thrombocythemia (ET) patients.Methods This study was a retrospective cohort study including PV and ET patients diagnosed by WHO criteria and treated with HU between January 2000 and June 2020. Clinical features, laboratory data, and resistance or intolerance of HU were collected. The prevalence, clinical outcomes, and associated factors of HU resistance or intolerance were analyzed.Results There were 260 patients including 144 ET and 116 PV. The prevalence of HU resistance or intolerance was 11.9% (31 patients) which was more frequent in ET patients (14.6% vs. 8.6% in PV). Patients who had HU resistance or intolerance significantly increased the risk of bleeding events (HR 2.64; 95% CI 1.19–5.85, P = 0.017). The risk factors of HU resistance or intolerance were low baseline hemoglobin levels (HR 0.90; 95%CI 0.84–0.97, P = 0.01), age more than 60 years old (HR 3.98; 95% CI 2.08–7.62, P < 0.001) and splenomegaly (HR 2.08; 95% CI 1.03–4.21, P = 0.04).Conclusions The prevalence of HU resistance or intolerance in PV and ET patients was 11.9%. Patients with HU resistance or intolerance significantly increased the risk of bleeding complications.