The aim of the study is to present a method to build an octree and to query from it for huge 3D point clouds of which volumes correspond or surpass the main memory, based on the memory-efficient octree developed by Han(2013). To the end, the method directly refers to 3D point cloud stored in a file on a hard disk drive instead of referring to that duplicated in the main memory. In addition, the method can save time to rebuild octree by storing and restoring it from a file. The memory-referring method and the present file-referring one are analyzed using a dataset composed of 18 million points surveyed in a tunnel. In results, the memory-referring method enormously exceeded the speed of the file-referring one when generating octree and querying points. Meanwhile, it is remarkable that a still bigger dataset composed of over 300 million points could be queried by the file-referring method, which would not be possible by the memory-referring one, though an optimal octree destination level could not be reached. Furthermore, the octree rebuilding method proved itself to be very efficient by diminishing the restoration time to about 3% of the generation time.