Despite medical progress, mortality from gastrointestinal perforation was relatively high. Our study's objective was to identify risk factors associated with a poor prognosis for gastrointestinal perforation. Patients diagnosed with gastrointestinal perforation at the Longchuan County People's Hospital between January 2019 and February 2022 were the subject of a retrospective analysis of their laboratory data. Patients were grouped based on length of hospital stay, septic shock, and mortality. A total of 240 patients participated in our study. Using univariate and multivariate analysis, we identified several risk factors for gastrointestinal perforation associated with a dismal prognosis. Lower digestive tract perforation (OR=2.418, 95% CI 1.119-5.227, P=0.025), low total protein (OR=0.934, 95% CI 0.879-0.992, P=0.026) and low hemoglobin (OR=0.985, 95% CI 0.971-0.999, P=0.039) were linked to a longer length of stay, especially hemoglobin (OR=0.978, 95% CI 0.966-0.991, P=0.001) in upper digestive tract. High ratio of neutrophils to lymphocytes (NLR) (OR=1.043, 95% CI 1.012-1.076, P=0.007), high lymphocyte-to-monocyte ratio (LMR) (OR=2.158, 95% CI 1.495-3.115, P<0.001) and low prognostic nutrition index (PNI) (OR=0.814, 95% CI 0.751-0.833, P<0.001) predicted septic shock. In upper digestive tract, PLR (OR=1.001, 95% CI 1.000-1.002, P=0.067), LMR (OR=2.160, 95% CI 1.440-3.240, P<0.001) and PNI (OR=0.843, 95% CI 0.767-0.926, P<0.001) were risk factors for septic shock, and total protein (OR=0.796, 95% CI 0.686-0.923, P=0.003) was a risk factor for septic shock in lower digestive tract. High NLR (OR=1.056, 95% CI 1.019-1.093, P=0.003), high LMR (OR=1.760, 95% CI 1.177-2.632, P=0.006) and low PNI (OR=0.832, 95% CI 0.754-0.918, P<0.001) were the risk factors of mortality. In subgroup analysis of perforation site, albumin (OR=0.820, 95% CI 0.719-0.934, P=0.003) and LMR (OR=1.506, 95% CI 1.069-2.123, P=0.019) were risk factors for mortality in upper digestive tract and PNI (OR=0.636, 95% CI 0.445-0.908, P=0.013) was a risk factor for mortality in lower digestive tract. Our research found that the perforation site, total protein, albumin, hemoglobin, NLR, LMR, PLR and PNI were risk factors for gastrointestinal perforation with a poor prognosis.