Many countries encountered “barriers” or obstacles that hampered the process of adapting to the integrated flood risk management (IFRM) from the traditional hard structural solutions in managing urban flooding. One of the crucial tasks to overcome the barriers is to understand their interrelationships. However, analysis of the interrelationships between the barriers to IFRM adaptation has not been carried out yet. This study attempts to analyze the interrelationships between the barriers to IFRM adaptation using the Interpretive Structural Modeling (ISM) method. The barriers in Metro Manila, a megacity in a developing country, were identified first in this study. Then, the ISM method was slightly modified and applied to analyze the interrelationships of the identified barriers. As a result, we identified 12 barriers which are relatively numerous compared with the developed countries, and so we categorized them into the governance, social, and technological resources aspects. Through the application of the ISM method, the interrelationships of the barriers to IFRM adaptation were systematically analyzed for the first time while also showing their hierarchical diagram. The results of the ISM reveal that barriers in the governance aspect are the most influential in which the lack of a sole organizing body is the most influential barrier. The barriers in the technological resources aspect are the second most influential, while barriers in the social aspect are the least influential and most dependent barriers. The approach presented in this study can be useful for decision makers and practitioners in understanding the interrelationships between the barriers.