This study aims to clarify the mechanism of storm surge caused by low-pressure systems, which differ from typical storm surges associated with typhoons and have been prominently observed along the northern coast of Kyushu, Japan. An integrated approach was employed by combining the analysis of observational data with numerical simulations using an ocean circulation model. First, based on tide gauge and wind data collected at multiple locations along the Northern Coast of Kyushu, the temporal relationship between storm surge anomalies and wind variations was evaluated. A strong correlation was identified between the rotational component of wind direction and the amplitude of the anomalies. Subsequently, numerical simulations using realistic coastal topography successfully captured the characteristics of coastal wave propagation (i.e. coastal-trapped gravity waves) generated by wind rotation and coastal geometry, and accurately reproduced both the timing and amplitude of the storm surge anomalies in the gauge. Furthermore, numerical experiments using idealized topographic meshes and simplified wind conditions quantitatively assessed how the rotation period of wind and the presence or absence of topographic features affect the resonant amplification or suppression of storm surges. In particular, it was revealed that the Goto Islands contribute to the earlier formation and amplification of storm surges, while the Korean Peninsula suppresses wave amplitude by limiting the spatial extent of wave propagation. These findings contribute to a better understanding of storm surge mechanisms anywhere in the world, including regions with similar geographic settings, and provide valuable insights for enhancing the accuracy of anomaly prediction models and strengthening disaster prevention and mitigation strategies.