Objective To reclassify intramuscular hemangioma patients with the International Society for the Study of Vascular Anomalies (ISSVA) criteria, and compare the clinicopathological differences between different types. Methods Intramuscular hemangioma cases diagnosed using the World Health Organization (WHO) classification of soft tissue and bone tumors were collected from Oct. 2013 to May 2021 in The First Affiliated Hospital of Xinjiang Medical University and re-classified as hemangioma or vascular malformations with the ISSVA criteria. The clinicopathological characteristics were compared between the 2 groups. Results A total of 40 intramuscular vascular cases diagnosed using the WHO criteria were enrolled, including 4 hemangioma cases and 36 vascular malformation cases reclassified by the ISSVA criteria. The hemangioma cases were mainly female (1 male and 3 females) and were mainly in the head and neck region (4 cases all in the face). The patients with vascular malformations were mainly venous malformations (22 venous malformations, 1 arteriovenous malformation, and 13 mixed vascular malformations). The lesions were more commonly seen in the extremities, especially in the lower limbs (19 in the lower limbs, 10 in the upper limbs, 4 in the trunk, and 3 in the face). The pathological morphology of hemangioma was characterized by vascular proliferation with lobed distribution under the microscope, in which vascular endothelial cells were plump and mitosis could be seen. While the microscopic morphological features were correlated with the specific subtype of vascular malformations, venous malformations were characterized by thin-walled and dilated veins, occasionally accompanied by thrombosis and phleboliths. The thickness of blood vessels varied for arteriovenous malformations, with fibers and smooth muscles proliferating into surrounding stroma. For lymphatic malformations, the diameters of lymphatics differed and foci of lymphocytic cells could be seen in the stroma. There was no recurrence in hemangioma patients, and the recurrence rate was 22.2% (8/36) for vascular malformation cases during the follow-up from 9 months to 8 years. Conclusion It is suggested to reclassify intramuscular hemangiomas with the ISSVA criteria. The new classification (hemangioma and vascular malformation) has significant differences in lesion location, prognosis and pathological morphology.