AbstractBase isolation is one of the most efficient methods for seismic mitigation of building and bridge structures in high‐intensity areas. However, the base‐isolated structure designed according to current codes based on the local seismic hazard and a few station records might not guarantee the performance of the base isolation system and ensure the safety of the structure. Carrying out a probabilistic analysis of seismic mitigation of base‐isolated structures, considering the randomness associated with earthquake ground motions, is thus necessary. To this end, the stochastic seismic response and reliability analysis of base‐isolated structures subjected to stochastic ground motions are conducted in this study, in conjunction with the probability density evolution method and the principle of equivalent extreme value event. The recently developed sliding hydromagnetic bearing is employed to constitute the base isolation layer of the base‐isolated structure. A refined finite element analysis is carried out to accurately reveal the dynamic characteristics of the base‐isolated structure. It is shown that the base‐isolated structure can be well simulated by the finite element model, which is verified through a comparative study with the results of shaking‐table tests. The base‐isolated structure gains a sound seismic mitigation compared to the base‐fixed structure in a probabilistic sense, and can ensure the safety of the structure by deploying a moderately designed base isolation system.