On Tuesday, January 17, 1995, an earthquake of magnitude 7.2 struck the Port of Kobe. In effect, the port was practically destroyed. After a hazard investigation, researchers reached a consensus to adopt a performance-based design in port and harbor structures in Japan. A residual displacement of geotechnical structures after an earthquake is one of the most important engineering demands in performance-based earthquake-resistant design. Thus, it is essential to provide reliable responses of geotechnical structures after an earthquake through various techniques. Today, a nonlinear explicit response history analysis(NERHA) of geotechnical structures is the most efficient way to achieve this goal. However, verification of the effective stress analysis, including post liquefaction behavior, is difficult to perform at a laboratory scale. This study aims to rigorously verify the NERHA by using well-defined field measurements, existing numerical tools, and constitutive models. The man-made, Port Island, in Kobe provides intensive hazard investigation data, strong motion records of 1995 Kobe earthquake, and sufficient engineering parameters of the soil. Two dimensional numerical analysis was conducted on the caisson quay wall section at Port Island subjected to the 1995 Kobe earthquake. The analysis result matches very well with the hazard investigation data. The NERHA procedure presented in this paper can be used in further studies to explain and examine the effects of other factors on the seismic behavior of gravity quay walls in liquefiable soil areas.