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Structural control and health monitoring scheme play key roles not only in enhancing the safety and reliability of infrastructure systems when they are subjected to natural disasters, such as earthquakes, high winds, and sea waves, but it also optimally minimize the life cycle cost and maximize the whole performance through the full life cycle design. In this scheme, system identification is regarded as a major technique to identify system states and related parameter variables, thus preventing degradation of structural or mechanical systems when unexpected disturbances occur. In this paper, three different strategies are proposed to identify general hysteretic behavior of a typical shear structure subjected to external excitations. Different case studies are presented to analyze the dynamic responses of a time varying shear structural system with the early version of Bouc-Wen-Baber-Noori (BWBN) hysteresis model. By incorporating a “Gray Box” strategy utilizing an Intelligent Parameter Varying (IPV) and Artificial Neural Network (ANN) approach, a Genetic algorithm (GA), and a Transitional Markov Chain Monte Carlo (TMCMC) based Bayesian Updating framework system identification schemes are developed to identify the hysteretic behavior of the structural system. Hysteresis characteristics, computational accuracy, and algorithm efficiency are further discussed by evaluating the system identification results. Results show that IPV performs superior computational efficiency and system identification accuracy over GA and TMCMC approaches.