The seismic reliability calculation of complex building structures requires a lot of simulation analysis and therefore the calculation cost is high. Fitting performance function with surrogate model can improve computational efficiency, but how to ensure the calculation accuracy while improving the reliability analysis efficiency of the engineering structure is a problem worthy of study. This paper proposes a Kriging-based reliability analysis method, which establishes the Kriging surrogate model with fewer calculations of the performance function, improves the accuracy of the surrogate model of performance function by infill-sampling, and obtains the approximate failure probability combined with Monte Carlo simulation. Two numerical examples are analyzed; the results show that this method is efficient and accurate. The method is applied to the seismic reliability calculation of mega-sub controlled structural system, in which the randomness of structure and seismic action is considered. The application results show that it is an effective method for reliability analysis of complex building structures.