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Iron deficiency (ID) prevalence in Chinese patients suffering from pulmonary hypertension (PH) is unclear so far. This study aimed to investigate ID prevalence in different subtypes of PH and its relevant factors.Hospitalized patients diagnosed with PH from September 2015 to March 2017 were retrospectively enrolled. Patients were grouped based on etiology. Logistic regression analysis was performed to determine factors associated with ID.ID was found in 38.25% of 251 PH patients; with the highest prevalence in connective tissue disease associated pulmonary arterial hypertension (CTD-PAH). Univariate logistic regression analysis showed that female sex, age, CTD-PAH diagnosis and high sensitive C reactive protein (hs-CRP) were associated with ID. After adjusting for age, sex and hs-CRP, the diagnosis of CTD-PAH was still associated with ID (OR = 3.01, 95%CI 1.02–8.90, P < 0.05).ID is common in PH in China. CTD-PAH is independently associated with ID, after adjustment for age, sex, and hs-CRP.