Computed tomography (CT) technology has been gradually used in the differentiation of small mesenchymal tumors of the stomach and intestines from smooth muscle tumours. To explore the value of enhanced CT in the differentiation of small mesenchymal tumors of the stomach and intestines from smooth muscle tumours. Clinical data of patients with gastric mesenchymal or gastric smooth muscle tumours who were treated in our hospital from May 2018 to April 2023 were retrospectively analysed. Patients were divided into the gastric mesenchymal tumor group and the gastric smooth muscle tumor group respectively (n = 50 cases per group). Clinical data of 50 healthy volunteers who received physical examinations in our hospital during the same period were selected and included in the control group. Serum levels of carcinoembryonic antigen (CEA), alpha-fetoprotein (AFP), carbohydrate antigen 19-9 (CA19-9), CA-125 and cytokeratin 19 fragment antigen 21-1 were compared among the three groups. The value of CEA and CA19-9 in the identification of gastric mesenchymal tumours was analysed using the receiver operating characteristic (ROC) curve. The Kappa statistic was used to analyse the consistency of the combined CEA and CA19-9 test in identifying gastric mesenchymal tumours. CEA levels varied among the three groups in the following order: The gastric mesenchymal tumour group > the control group > the gastric smooth muscle tumour group. CA19-9 levels varied among the three groups in the following order: The gastric mesenchymal group > the gastric smooth muscle group > the control group, the difference was statistically significant (P < 0.05). ROC analysis showed that the area under the curve of CEA and CA19-9 was 0. 879 and 0. 782, respectively. Enhanced CT has shown value in differentiating small mesenchymal tumors of the stomach and intestines from smooth muscle tumors.