The present invention is to provide a system and a method for index reorganization using a partial index transfer in a spatial data warehouse that minimize costs of search, split and readjustment for the index reorganization by organizing and transferring clusters with partial indexes in conformity with an index structure so that the partial indexes can be inserted directly into the existing index, thus ensuring continuous and stable data processes, the index reorganization method comprising: a first step of clustering data extracted from the source database in conformity with an index structure via the builder; a second step of generating partial indexes and transferring the partial indexes to a cluster generated according to the clustering; a third step of recording the transferred partial indexes in physically consecutive spaces, not allocated, in the spatial data warehouse server; and a fourth step of inserting the recorded partial indexes in an existing index.