Objective To investigate the features of endoscopic ultrasonography in the diagnosis of malignant mediastinal and abdominal lymphadenopathy and to provide more evidence for endoscopic ultrasound-guided fine-needle aspiraiton (EUS-FNA). Methods A case-control study was performed on 83 consecutive patients who underwent EUS in the Second Affiliated Hospital of Soochow University from September 2016 to February 2021. Lymph node properties were identified by pathological results of EUS-FNA and (or) surgery and follow-up for at least 6 months. According to the final diagnosis, patients were divided into malignant lymph node group (n=56) and benign lymph node group (n=27). Univariate analysis and multivariate logistic analysis were performed to identify independent risk factors for malignant lymphadenopathy in terms of EUS features. Results Univariate analysis showed that the length of short axis, short-long axis ratio, shape, border, presence or absence of hilum, heterogeneous echo, and the growth pattern of lymph node were risk factors for malignant lymph nodes (P<0.10). Multivariate logistic regression analysis showed that short axis>10 mm (P=0.021, OR=9.751, 95%CI: 1.407-57.573), clear border (P=0.009, OR=20.587, 95%CI: 2.149-197.251), absence of hilum (P=0.019, OR=28.502, 95%CI: 1.725-470.864), nodal matting (P=0.004, OR=45.539, 95%CI: 3.429-604.822), partial nodal fusion (P=0.004, OR=50.012, 95%CI: 3.497-715.266) were independent risk factors for malignant mediastinal and abdominal lymph nodes. Conclusion EUS is useful to differentiate the lymph node properties in the mediastinal or abdominal cavity. Short axis>10 mm, clear border, absence of hilum, nodal matting and partial nodal fusion are high-risk EUS features of malignant mediastinal or abdominal lymphadenopathy, where priority should be given to EUS-FNA.