During the past 20 years of Macao's return to the motherland, rapid development of the society and the economy, acceleration of land reclamation projects, and the continuously congregated population of coastal zones have led to tremendous changes in urban ecosystem patterns. Based on two high-resolution remote sensing images of 2001 and 2017, the land use transfer matrix and the center of gravity transfer were analyzed. Then optimum analysis granularity was determined by the granularity push method, and spatial and temporal changes of urban ecological system patterns were studied by the moving window method. Finally, combined with field investigations, research findings were discussed. The results indicated that:(1) the total land area of Macao expanded from 26.19 km² to 32.77 km², with a growth rate of 25.12%, of which bare land and construction land expanded significantly; (2) the urban ecological system of Macao was greatly affected by human disturbance, which resulted in the increase of the urban landscape fragmentation, the decrease of diversity, the complex and irregular landscape shape, and the risk of the decline in the quality of urban habitats; (3) landscape composition and the spatial structure of the Macao Peninsula and Islands were significantly different, and their dominant landscapes were construction land and forest land, respectively; and (4) the main reclamation method in Macao peninsula was islands reclamation, while coastal reclamation was the main reclamation method in the Island area.