This study aimed to develop a comprehensive prediction model integrating polygenic risk scores (PRS) and clinical factors to identify individuals at high risk for incident idiopathic pulmonary arterial hypertension (IPAH). A PRS was constructed using summary statistics derived from the largest genome-wide association study for pulmonary arterial hypertension in Europeans and validated in the UK Biobank (732 cases, 458,258 controls). After excluding individuals with IPAH at baseline, 316,073 participants (316 incident IPAH patients) were split into training and testing sets (7:3). Variable selection was performed using least absolute shrinkage and selection operator in the training set, and a prediction model for incident IPAH was established using the Cox proportional hazards model. The dataset here is the Supplementary Data for the manuscript titled "Polygenic risk score and clinical factors predict incident idiopathic pulmonary arterial hypertension". The dataset contains the weight for each single-nucleotide polymorphism used for constructing PRS for IPAH.