East Johor is characterized by an embayed coastline between headlands facing the South China Sea. Like any other countries and regions with coastal lowland areas, the threat of climate change especially sea level rise (SLR) and storm surge (SS) are considered the millennium challenges to the east coast of Johor (EJ). The coupled climate effect is rarely investigated and acknowledged theoretically or numerically, which called for an immediate attention to identify the dual SS-SLR impact on the vulnerability of the coast and the feasible protection required. The present study adopted the fundamental Physical Vulnerability Index (PVI) to assess the coastal vulnerability for EJ. Through hydrodynamic modelling of typhoon-induced surge, SS height is extracted for several scenarios of a single storm track in different wind speed and SLR projections. The utilization of a survey data, land use and lithology maps are anticipated to assist in providing the vulnerability indicators for physical variable, such as coastal slope and elevation, coastline landforms or features and marine depth, as well as the SS and SLR. The weight and scores for PVI are calculated using the analytical hierarchy process (AHP) method, an improvement to the methodology for assessing the vulnerability of a coast of interest. A coastal vulnerability cartograph is developed to demarcate the two distinctive districts of the east Johor with five specific vulnerable ranks from very low (1), low (2), medium (3), high (4) and very high risk (5). Based on the SS model, the increased in typhoon wind speed is unparalleled with SS height. But the rise in sea level intensify the surge magnitude which exaggerated the already vulnerable of the unprotected coast. In other words, changes in vulnerability correlates to severity in damage and an increase in SS-SLR has its inherent risk to coastal communities. Thus, coastal protective measures, from shorefront to offshore barriers is an essential consideration to be exercised to decrease future coastal flood risk and erosion along the coastal lowland area of east Johor. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd 2023.