Background The clinical characteristics and prognosis of primary intestinal diffuse large B-cell lymphoma (PI-DLBCL) are rarely reported. We aimed to explore the role of surgery in patients with PI-DLBCL. Methods Adult PI-DLBCL patients were included from the Surveillance, Epidemiology, and End Results database. The effect of surgery was evaluated by Kaplan-Meier and Cox proportional regression analyses. Propensity score matching (PSM) was used to reinforce our results. Lasso regression was utilized to determine independent risk factors of overall survival (OS) for a nomogram and a novel web-based calculator. The performance of the model was measured via concordance index, receiver operating characteristic curve, and calibration plots in both cohorts. Results Overall, 1602 patients with PI-DLBCL were analyzed. Surgery significantly improved survival in both univariate and multivariate analyses (p = 0.007, p < 0.001, respectively). Before PSM, local tumor destruction (LTD) displayed a survival advantage over resection in patients without chemotherapy (p = 0.034). After PSM, surgery was still identified as a beneficial factor for OS (p = 0.0015). However, there was no statistical difference between LTD and resection (p = 0.32). The nomogram for 3-, 5-, and 10-year OS predictions exhibited dependable consistency between internal and external validation. Conclusion This study approves the beneficial effect of surgery on clinical endpoints in PI-DLBCL patients. For those who are not suitable for resection, LTD may also be a practical option. The predictive nomogram and the web-based calculator could help clinicians individually evaluate the prognosis and optimize personalized treatment decisions for these patients.