To evaluate the value of simplified pulmonary embolism severity index (sPESI) , brain natriuretic peptide (BNP) and high-sensitivity troponin I (hs-TnI) in predicting the short-term and long-term prognosis of patients with acute pulmonary embolism.We collected the clinical data of 162 consecutive patients with acute pulmonary embolism in The First Affiliated Hospital of Dalian Medical University from January of 2010 to September of 2012. Hospital death, shock, mechanical ventilation and cardiopulmonary resuscitation were defined as the primary endpoints while death within 38 months as the secondary endpoint. The correlations between sPESI,BNP and hs-TnI, and the primary and secondary endpoints in the overall cohort and hemodynamically stable subgroup were analyzed respectively.BNP, hs-TnI and sPESI were independent predictors in multivariate regression of the primary endpoints in the overall cohort. The area under ROC curve and the risk odds ratio of them were 0.87, 8.16;0.91, 6.09 and 0.78 , 14.07 respectively.Only BNP and sPESI were independent predictors in multivariate regression of the primary endpoints in hemodynamically stable subgroup.Only sPESI was an independent risk factor in COX regression of the secondary endpoint. The combination of BNP and hs-TnI further improved the positive predictive value (44.4%), while the negative predictive value was unaffected(97.8%). There was no adverse event in patients with low score of sPESI and single-positive or negative combination of BNP and hs-TnI.sPESI could reflect overall risk of pulmonary embolism.It had a high value in the evaluation of pulmonary embolism prognosis, especially for long-term prognosis.It should be integrated into the risk stratification strategy of pulmonary embolism.In the evaluation of short-term prognosis, BNP and hs-TnI were the best indicators, and the combination of BNP, hs-TnI and sPESI could further improve the prognostic value.