Marine macroinvertebrates are essential organisms that contribute significantly to the structure and function of aquatic ecosystems such as coral reef. This study examined the relationship between substrate types and macroinvertebrate communities in the Sempu Strait, Malang, to understand the ecological interactions within the coral reef ecosystems. Using belt transect and quadrat transect methods, macroinvertebrate species were recorded and analyzed for their diversity, density, and distribution across different substrates, such as hard coral, macroalgae, dead coral, sand, and rubble. The data conducted in 5 stations in Sempu Strait. The findings revealed that hard coral and macroalgae positively influenced macroinvertebrate abundance, whereas dead coral and muddy substrates were associated with lower diversity and density. A total of 706 macroinvertebrates were recorded, belonging to six classes and 16 genera. Among the stations, the Floating House station exhibited the highest coral cover and macroinvertebrate abundance, while the Jetty station had the highest dominance of Diadema and the lowest diversity, suggesting a disturbed habitat. The Principal Component Analysis (PCA) demonstrated significant relationships between substrate types and the abundance of specific macroinvertebrate species. For example, the Tridacna clam showed a positive correlation with macroalgae, while Diadema was more prevalent on silt and dead coral substrates. The study emphasizes the importance of substrate complexity in supporting macroinvertebrate diversity and highlights the need for maintaining healthy coral reef ecosystems to preserve biodiversity in the Sempu Strait.