The heterogeneity nature of sepsis is significantly impacted by the site of infection. This study aims to explore the predictive value of multiple scoring systems in assessing the prognosis of septic patients across different infection sites. Data for this retrospective cohort study were extracted from the Medical Information Mart for Intensive Care IV database (MIMIC-IV) (v2.2). Adult patients meeting the criteria for sepsis 3.0 and admitted to the intensive care unit (ICU) were enrolled. Infection sites included were pneumonia, urinary tract infection (UTI), cellulitis, abdominal infection, and bacteremia. The primary outcome assessed was 28-day mortality. The sequential Organ Failure Assessment (SOFA) score, Oxford Acute Severity of Illness Score (OASIS), and Logistic Organ Dysfunction System (LODS) score were compared. Binomial logistic regression analysis was conducted to evaluate the association between these variables and mortality. Additionally, differences in the area under the curve (AUC) of receiver operating characteristic (ROC) among the scoring systems were analyzed. A total of 4721 patients were included in the analysis. The average 28-day mortality rate was 9.4%. Significant differences were observed in LODS, OASIS, and SOFA scores between the 28-day survival and non-survival groups across different infection sites (p < 0.01). In the pneumonia group and abdominal infection group, both the LODS and OASIS scoring systems emerged as independent risk factors for mortality in septic patients (odds ratio [OR]: 1.165, 95% confidence interval [CI]: 1.109-1.224, p < 0.001; OR: 1.047, 95% CI: 1.028-1.065, p < 0.001) (OR: 1.200, 95% CI: 1.091-1.319, p < 0.001; OR: 1.060, 95% CI: 1.025-1.095, p < 0.001). For patients with UTI, the LODS, OASIS, and SOFA scoring systems were identified as independent risk factors for mortality (OR: 1.142, 95% CI: 1.068-1.220, p < 0.001; OR: 1.062, 95% CI: 1.037-1.087, p < 0.001; OR: 1.146, 95% CI: 1.046-1.255, p = 0.004), with the AUC of LODS score and OASIS significantly higher than that of the SOFA score (p = 0.006). Among patients with cellulitis, the OASIS and SOFA scoring systems were identified as independent risk factors for mortality (OR: 1.055, 95% CI: 1.007-1.106, p = 0.025; OR: 1.187, 95% CI: 1.005-1.403, p = 0.044), with no significant difference in prognosis prediction observed (p = 0.243). In the bacteremia group, the LODS scoring system was identified as an independent risk factor for mortality (OR: 1.165, 95% CI: 1.109-1.224, p < 0.001). The findings suggest that LODS scores offer better prognostic accuracy for predicting the mortality risk in septic patients with pneumonia, abdominal infections, bacteremia, and UTI compared to SOFA scores.