This work seeks the development and validation of radiomics signatures from nonenhanced computed tomography (CT, NE‐RS) to preoperatively predict the malignancy degree of gastrointestinal stromal tumors (GISTs) and the comparison of these signatures with those from contrast‐enhanced CT. A dataset for 370 GIST patients was collected from four centers. This dataset was divided into cohorts for training, as well as internal and external validation. The minimum‐redundancy maximum‐relevance algorithm and the least absolute shrinkage and selection operator (LASSO) algorithm were used to filter unstable features. (a) NE‐RS and radiomics signature from contrast‐enhanced CT (CE‐RS) were built and compared for the prediction of malignancy potential of GIST based on the area under the receiver operating characteristic curve (AUC). (b) The radiomics model was also developed with both the tumor size and NE‐RS. The AUC values were comparable between NE‐RS and CE‐RS in the training (.965 vs .936;
P
= .251), internal validation (.967 vs .960;
P
= .801), and external validation (.941 vs .899;
P
= .173) cohorts in diagnosis of high malignancy potential of GISTs. We next focused on the NE‐RS. With 0.185 selected as the cutoff of NE‐RS for diagnosis of the malignancy potential of GISTs, accuracy, sensitivity, and specificity for diagnosis high‐malignancy potential GIST was 90.0%, 88.2%, and 92.3%, respectively, in the training cohort. For the internal validation set, the corresponding metrics are 89.1%, 94.9%, and 80.0%, respectively. The corresponding metrics for the external cohort are 84.6%, 76.1%, and 91.0%, respectively. Compared with only NE‐RS, the radiomics model increased the sensitivity in the diagnosis of GIST with high‐malignancy potential by 5.9% (
P
= .025), 2.5% (
P
= .317), 10.5% (
P
= .008) for the training set, internal validation set, and external validation set, respectively. The NE‐RS had comparable prediction efficiency in the diagnosis of high‐risk GISTs to CE‐RS. The NE‐RS and radiomics model both had excellent accuracy in predicting malignancy potential of GISTs.