As a valuable resource in coastal areas, coastlines are not only vulnerable to natural processes such as erosion, siltation, and disasters, but are also subjected to strong pressures from human processes such as urban growth, resource development, and pollution discharge. This is especially true for reef nations with rich coastline resources and a large population, like Indonesia. The technical joint of remote sensing (RS) and geographic information system (GIS) has significant advantages for monitoring coastline changes on a large scale and for quantitatively analyzing their change mechanisms. Indonesia was taken as an example in this study because of its abundant coastline resources and large population. First, Landsat images from 1990 to 2018 were used to obtain coastline information. Then, the index of coastline utilization degree (ICUD) method, the changes in land and sea patterns method, and the ICUD at different scales method were used to reveal the spatiotemporal change pattern for the coastline. The results found that: (1) Indonesia’s total coastline length has increased by 777.40 km in the past 28 years, of which the natural coastline decreased by 5995.52 km and the artificial coastline increased by 6771.92 km. (2) From the analysis of the island scale, it was known that the island with the largest increase in ICUD was Kalimantan, at the expense of the mangrove coastline. (3) On the provincial scale, the province with the largest change of ICUD was Sumatera Selatan Province, which increased from 100 in 1900 to 266.43 in 2018. (4) The change trend of the land and sea pattern for the Indonesian coastline was mainly expanded to the sea. The part that eroded to the land was relatively small; among which, Riau Province had the most significant expansion of land area, about 177.73 km2, accounting for 23.08% of the increased national land area. The worst seawater erosion was in the Jawa Barat Province. Based on the analysis of population and economic data during the same period, it was found that the main driving mechanism behind Indonesia’s coastline change was population growth, which outweighed the impact of economic development. However, the main constraint on the Indonesian coastline was the topographic factor. The RS and GIS scheme used in this study can not only provide support for coastline resource development and policy formulation in Indonesia, but also provide a valuable reference for the evolution of coastline resources and environments in other regions around the world.