Background: Pulmonary embolism (PE) remains a major cause of morbidity and mortality in critical care, yet traditional diagnostic methods face limitations, especially in critically ill patients. This study introduces a novel frequency-domain band-pass filtering enhanced electrical impedance tomography (EIT) pulsation method for rapid, non-invasive PE diagnosis and risk stratification. Methods: In a two-center retrospective study, 106 participants (53 PE patients, 53 healthy controls) were enrolled. A 16-electrode EIT system recorded pulmonary blood flow pulsation signals, with a heart rate-adaptive 0.8–2 Hz band-pass filter to mitigate respiratory and motion artifacts. Key parameters (Matching Index （MI）, Dispersion Index (DI), Shunt Index (SI), Electrical Impedance VQ ratio(EVIQ)) were analyzed for PE diagnosis and risk stratification. Results: PE patients showed significantly lower MI and higher DI and SI compared to controls (P<0.001). For risk stratification, intermediate-high-risk PE patients had notably lower MI and higher DI than lower-risk groups (P<0.001). The combined MI+DI+SI model demonstrated the highest diagnostic efficacy for PE (AUC=0.820, 95% CI: 0.739–0.892), outperforming individual parameters. EIVQ showed no significant discriminative value. Conclusions: The enhanced EIT pulsation method effectively mitigates respiratory and motion artifacts. MI, DI, and SI are reliable non-invasive parameters for PE diagnosis and risk stratification, offering a practical bedside tool in critical care.