The effect of beaded caverns on vertical bearing characteristics of pile foundation was investigated. The load-settlement characteristics, variation rule of vertical ultimate bearing capacity, distribution rule of pile axial force, side resistance, and partial load of piles under different roof thickness-pile diameter ratios were studied by centrifugal model test, when the pile passed through two layers of caves and there was an underlying cave. A reasonable method for calculating roof thickness-pile diameter ratio was proposed by comparing with the test results of the case without underlying karst cave. Results show that when the pile passed through the cavern, the roof thickness to pile diameter ratio of the underlying caverns had a great influence on the vertical ultimate bearing capacity of the pile. When the roof thickness-pile diameter ratio increased from 0.5 to 3.0, the influence degree of vertical ultimate bearing capacity of the pile decreased from 57.4% to 4.0% compared with the case without karst cave. When the roof thickness-pile diameter ratio was greater than 2.5, the influence degree of vertical ultimate bearing capacity of the pile was less than 5.0%. When the roof thickness-pile diameter ratio increased, the axial force of the pile was almost not attenuated in the cavern. The decay rate of the axial force of the pile in the upper and middle cave roof was slow, and the load transmitted to the cave roof was large. The side resistance of the pile barely had influence in the cave that the pile passed through. With the increase in the roof thickness-pile diameter ratio, the side resistance of the pile decreased in the upper and middle cave roof. As the roof thickness-pile diameter ratio increased, the proportion of pile side resistance and pile tip resistance gradually decreased and increased, and the pile gradually transformed to frictional end bearing pile. When the roof thickness-pile diameter ratio was greater than 2, the side resistance of the pile decreased less than 10% compared with the condition without underlying karst cave. In beaded karst cave area, when the pile passes through two-layer karst caves and is above an underlying karst cave, it is recommended that the influence of the underlying karst cave on the vertical bearing characteristics of the pile can be ignored if the roof thickness-pile diameter ratio is great than 2.5, and a reasonable roof thickness can be determined according to the bearing requirements of the pile foundation.