3D geometry is an essential concept in mathematics because it relates to real-world experiences and numerous mathematical topics. However, some students still have difficulty understanding this geometry. Therefore, this study aims to identify and describe students' epistemological obstacles to the dimensions of representation, spatial structure, and measurement of 3D geometry in junior high school. This study was carried out using an exploratory case study design with the purposive sampling method used to obtain data from 26 students from three junior high schools in Indramayu Regency, Indonesia, through tests and interviews. The data collected were analyzed, synthesized, and described based on the framework that had been prepared. The result showed that students experience epistemological obstacles in performing a series of 3D geometric thinking tasks. They experience difficulties translating the representative model from 2D to 3D and determining the number of unit cubes of the 3D shape. Meanwhile, in the measurement dimensions, students experience difficulties in calculating surface area and comparing volumes of 3D geometric shapes. Therefore, to minimize the epistemological obstacle experienced by students, this study suggests teachers or prospective teachers pay attention to the characteristics of the material to be taught to students.