The base isolation structure has a high requirement for integrity of the isolation layer, and the connection behavior of the isolation layer members affects the integrity and the seismic behavior of the isolation layer directly. In this paper, the welding connection mode between longitudinal reinforcements at the bottom of the beam was improved, the tensile tests were also carried out, and a new frame joint was proposed of the isolation layer for prefabricated concrete base isolation structure. Then, the finite element models of the new frame joint and traditional cast-in-place joint were established to simulate the seismic behavior and the structural integrity under the lateral repeated loads in ABAQUS. Finally, an improved connection mode for the new frame joint was proposed by comparing the difference of seismic behavior between the two kinds of joints. The results showed that the tensile strength of the specimen which connected by grooving and welding on the steel plate was close to that of the complete reinforcement, and could significantly reduce the bending deformation of the connecting steel plate. The bearing capacity, stiffness and energy dissipation capacity of the prefabricated frame joint were lower than that of the cast-in-place joint, but the deformation capacity was stronger. The bearing capacity, stiffness, and deformation capacity of the new frame joint on the prefabricated isolation layer increased when some anchored rebars were added to the ends of the prefabricated beam, the reinforcement ratio at the end of beams also increased, at the same time, the plastic development of the longitudinal reinforcement was delayed by the anchored rebars, so the energy dissipation capacity decreased. The load-bearing capacity, stiffness and deformation capacity of the improved prefabricated frame joint were all stronger than that of cast-in-place joint, so the improved new frame joint had an excellent structural integrity, and it could be used in practical engineering widely.