To characterize the morphological change in the right ventricle (RV) of patients with pulmonary artery hypertension (PAH) and further explore the correlation between septomarginal trabeculation (SMT) and right ventricular (RV) function, myocardial fibrosis, and exercise capacity in patients with PAH. Sixty untreated PAH patients were prospectively included from May 2016 to April 2017. All patients underwent comprehensive clinical evaluation and cardiac magnetic resonance (CMR). The area and diameter of the basal segment of SMT, and the mass of SMT were measured on cine SSFP images. Relationship between parameters of SMT and RV ejection fraction (RVEF), 6 min walking distance (6MWD), myocardial fibrosis and pulmonary vascular resistance (PVR) were evaluated by Pearson’s correlation and logistic regression. Predictive performance of SMT parameters for reduced RVEF or impaired 6MWD was evaluated by receiver operating characteristics (ROC) analysis. Compared with SMT diameter index and mass index, SMT area index (SMT Ai) in basal segment was the best parameter to show correlation with RVEF (r = − 0.496, P < 0.001), 6MWD (r = − 0.619, P < 0.001), and inferior insertion point (I IP) extracelluar volume (ECV) (r = 0.365, P = 0.008). ROC showed that SMT Ai had the strongest predictive value for reduced RVEF (AUC = 0.756), and impaired 6MWD (AUC = 0.813). SMT parameters were closely correlated with RV systolic function and 6MWD in patients with PAH. SMT Ai is a simple imaging indicator for the severity of PAH.