The tendency for internationalization of higher education in many Higher Education Institutions (HEIs) around the world, including those of Malaysia, is increasing with the current wave of globalization; however, the main challenge of international HEIs is how to manage intercultural diversity and overcome intercultural learning challenges that affect international students’ learning outcomes and learning sustainability. Hence, the aim of this study was to investigate intercultural learning challenges that affect international students’ learning sustainability through a proposed measurement model. The data were collected from 273 international students in Malaysian HEIs through a survey and were analyzed using variance-based structural equation modeling (i.e., PLS-SEM). The results showed that intercultural challenges did not have a significant effect on students’ learning sustainability. Nevertheless, language challenges, academic challenges, and research challenges were found to have a significant negative impact on the learning sustainability of international students. The study concluded that intercultural learning barriers are considered to be intercultural learning challenges, which have a negative effect on international students’ learning sustainability even though international students might overcome such challenges with the passage of time. In addition, the study identified different factors pertaining to international students’ learning sustainability, such as students’ language and learning skills, Higher Education Institutions’ educational systems, and lecturers. Based on the finding of the study, Higher Education Institutions need to create a clear framework that encompasses these factors to improve learning sustainability among international students.