In order to investigate the impact of land use information on ecosystem services, land use information of East Malaysia in 1990 and 2023 was obtained based on Landsat imagery, and the spatial and temporal characteristics of ecosystem services in East Malaysia over 30 years were analyzed using the InVEST model, which was combined with Pearson correlation and bivariate spatial autocorrelation analysis, to assess the synergistic relationship of trade-offs between the two. The results showed that natural forest was the land use type with the most obvious decrease, which was mainly converted into plantation forest and construction land; plantation forest had the most significant increase, which was mainly converted from natural forest, wetland, and grassland. The ecosystem service function showed a decreasing trend. The mean value of habitat quality is decreased by 0.09. Areas of better habitat quality were located in the eastern part of the study area, with a large distribution of natural forests. The area with poorer habitat quality is located in the coastal area, with construction land expanding in all directions centered on the key cities. The total carbon storage in the study area decreased by 1.6 × 108 t, mainly due to the transformation of natural forests to plantation forests and construction land. Habitat quality and carbon storage showed a synergistic relationship in spatial distribution.