This paper presents a hierarchical partitioning strategy (HP) for probability space to improve the accuracy of metamodel and avoid the memory problems of computer in dealing with small failure probability events. By the continuous partition of probability space, the construction of adaptive Kriging metamodel is intelligently divided into two steps. Thereafter, the well-trained Kriging via two steps is used to approximate the relationship between the extreme value of response and basic random variables of the system. By combining the probability density evolution method with well-trained Kriging metamodel, the reliability of the investigated stochastic system can be readily obtained with a one-dimensional integration operation. Subsequently, a new reliability analysis method is proposed, called HP-AK-PDEM (Hierarchical Partitioning strategy-based Adaptive Kriging combining Probability Density Evolution Method). To demonstrate the accuracy and efficiency of the proposed method, three analytical performance functions with nonlinear features and a ten-story shear-frame structure are addressed. The comparative study of different reliability methods is carried out as well. Numerical results demonstrate that the presented method has better accuracy and higher efficiency in dealing with the problems of small and rare failure probability issues encountered in engineering structures.