A high damping rubber bearing (HDRB) is widely utilized in base-isolation structures due to its good energy dissipation capacity and environmentally friendly properties; however, it is incapable of isolating the vertical vibration caused by earthquakes and subways effectively. Thick rubber bearings with a low shape factor have become one of the important vertical isolation forms. This paper provides an experimental comparative study on high damping rubber bearings with low shape factor (HDRB-LSF), thick lead–rubber bearings (TLRB), and lead–rubber bearings (LRB). The abilities of the bearing and energy dissipation of the above bearings are analyzed contrastively considering the influence of vertical pressure, loading frequency, shear strain, and pre-pressure. Firstly, the HDRB-LSF, TLRB, and LRB are designed according to the Chinese Code for seismic design of buildings. Secondly, cyclic vertical compression tests and horizontal shear tests, as well as their correlation tests, are conducted, respectively. The vibrational characteristics and hysteresis feature of these three bearings are critically compared. Thirdly, a corrected calculation of vertical stiffness for the thick rubber bearings is proposed based on the experimental data to provide a more accurate and realistic tool measuring the vertical mechanical properties of rubber bearings. The test results proved that the HDRB-LSF has the most advanced performance of the three bearings. For the fatigue property, the hysteresis curves of the HDRB-LSF along with TLRB are plump both horizontally and vertically, thus providing a good energy dissipation effect. Regarding vertical stiffness, results from different loading cases show that the designed HDRB-LSF possesses a better vertical isolation effect and preferable environmental protection than LRB, a larger bearing capacity, and, similarly, a more environmentally friendly property than TLRB. Hence, it can avoid the unfavorable resonance effect caused by vertical periodic coupling within the structure. All the experimental data find that the proposed corrected equation can calculate the vertical stiffness of bearings with a higher accuracy. This paper presents the results of an analytical, parametric study that aimed to further explore the low shape factor concepts of rubber bearings applied in three-dimensional isolation for building structures.