Background <p>This study analyzed preoperative CT features and postoperative pathological factors to predict recurrence after curative resection in primary gastrointestinal stromal tumor (GIST) and evaluate the prognostic validity of adjuvant therapy.</p> Methods <p>We retrospectively examined 718 patients with pathologically confirmed primary GISTs (mean age 57 ± 12.1&#xa0;years; range, 14–86&#xa0;years; 368 males, 350 females), who underwent R0 resection across two hospitals (internal set:<i> n</i> = 624; external set: <i>n</i> = 94). The internal set was randomly divided into training (<i>n</i> = 437) and validation cohorts (<i>n</i> = 187). Predictive efficacy of our nomogram was compared with the modified National Institutes of Health (MNIH) criterion using Kaplan–Meier analysis and multivariable Cox regression for recurrence-free survival (RFS).</p> Results <p>For recurrence prediction, AUC values for the CT model, combined nomogram (integrating CT features and pathological features), and MNIH criterion were 0.867/0.786/0.917 (training/validation/external test) and 0.890/0.810/0.953 versus 0.791/0.739/0.894, respectively. The combined nomogram demonstrated superior efficacy to the MNIH criterion across most probability thresholds (<i>P</i> &lt; 0.001). The prognostic nomogram stratified patients into ‘high-recurrence’ and ‘low-recurrence’ groups with significantly divergent RFS. In the training cohort, the 1-, 3-, 5-, and 7-year RFS rates of these two groups were 95.9%, 85%, 73.5%, and 62.2% versus 100%, 99%, 95.5%, and 95.5%, respectively (<i>P</i> &lt; 0.001). In the validation and external test cohorts, the nomograms were still significantly efficient (<i>P</i> &lt; 0.001).</p> Conclusions <p>The combined nomogram provides improved noninvasive prediction of GIST recurrence and prognosis compared to the MNIH criterion.</p> Trial registration <p>Approved by the Institutional Review Board of West China Hospital, Sichuan University (No. 2020-249).</p>