The invention discloses a method of three-dimensional geographic information system (GIS) terrain rendering. According to the method of the three-dimensional GIS terrain rendering, quad-tree partitioning is carried out on terrain data loaded from the three-dimensional GIS to generate rectangular grids of the terrain data, viewing pyramid cutting is carried out on the rectangular grids to obtain rectangular grids needed to be displayed, the rendering accuracy of each rectangular grid needed to be displayed is calculated and then is judged whether the rendering accuracy of each rectangular grid reaches a preset standard, then the quad-tree partitioning is carried out again on each rectangular grid which does not reach the preset standard, and for each rectangular grid reaching the preset standard, terrain units are generated and rendered according to the terrain data corresponding to each rectangular grid. The invention further discloses a system of the three-dimensional GIS terrain rendering correspondingly. The method and the system of the three-dimensional GIS terrain rendering can effectively improve the speed of the three-dimensional GIS terrain scene rendering, and enables the data processing process to be simpler and more rapid.