Objective To analyze features of color Doppler ultrasonography in gastrointestinal stromal tumors. Method The ultrasound images of gastrointestinal stromal tumors (51 cases) and gastrointestinal cancers (59 cases) confirmed by operation and pathology were compared and analyzed. Results The gastric stromal tumor mainly occurred at the bottom of the stomach and the body of the stomach (17 cases), the intestinal stromal tumor mainly occurred at the small intestine (24 cases). The gastric cancer mainly occurred at the gastric antrum (18 cases), the intestinal cancer all occurred at the colon (20 cases) and rectum (12 cases). Compared with the gastrointestinal cancers, the gastrointestinal cavity was not surrounded by tumor, the peripheral boundary was clear, the morphology was more regular, the internal echo was uneven, and there was no peripheral lymph node metastasis in the gastrointestinal stromal tumors, the differences were statistically significant (P<0.05). There were no significant differences in the degree of blood flow and tumor diameter between the gastrointestinal stromal tumors and the gastrointestinal cancers (P>0.05), but the blood flow of the intestinal stromal tumor was significantly more abundant as compared with the intestinal cancer (P<0.05). Conclusion Color Doppler ultrasonography, as a simple and rapid method, has a certain diagnostic value for differentiation of gastrointestinal stromal tumors and gastrointestinal cancers.