Objective To compare the prognostic value of different types of simplified Pulmonary Embolism Severity Index (sPESI) in patients with acute pulmonary embolism (APE), so as to select the best scoring system for clinical application. Methods We retrospectively collected the data of consecutive patients with APE in the Fourth People’s Hospital of Zigong City from January 1st, 2014 to January 1st, 2019. The endpoint was 1-month all-cause mortality. We tried to modify sPESI by replacing arterial oxyhaemoglobin saturation with arterial partial pressure of oxygen / fraction of inspired oxygen (new scoring system named psPESI), and modify sPESI by replacing arterial oxyhaemoglobin saturation with saturation of pulse oxygen / fraction of inspired oxygen (new scoring system named ssPESI), and analyzed the area under the receiver-operating characteristic curve (AUC), net reclassification improvement (NRI), integrated discrimination improvement (IDI), calibration and decision curve. Results A total of 280 patients (109 with low-risk APE, 155 with intermediate-risk APE, and 16 with high-risk APE) were enrolled in the study. Of these patients, 165 (58.93%) were male, and the 1-month all-cause mortality rate was 10.71% (30/280). The AUCs of sPESI, psPESI and ssPESI were 0.756, 0.822 and 0.807, respectively, and the AUC of ssPESI was higher than that of sPESI (P=0.038) but not lower than that of psPESI (P=0.388). Comparing ssPESI with sPESI, the NRI was 0.928 (P<0.001) and the IDI was 0.084 (P<0.001); comparing ssPESI with psPESI, the NRI was 0.041 (P=0.227) and the IDI was –0.028 (P=0.060). The psPESI (Hosmer-Lemeshow test χ2=12.591, P=0.182) and ssPESI (Hosmer-Lemeshow test χ2=4.204, P=0.897) were well-calibrated in the internal validation cohort and obtained more net benefits within wide threshold probabilities than sPESI. Conclusion Since the saturation of pulse oxygen is non-invasive and easy to obtain, and the predictive ability of ssPESI is similar to that of psPESI, it is recommended that ssPESI be used as a new scoring system to evaluate the prognosis of APE.