The present invention relates to a modular apparatus for cleaning a pet toilet device and, more specifically, to an apparatus for cleaning a pet toilet device, the apparatus being improved so as to prevent the problem of overflowing or unnecessary flow of water, and comprising three structures of: a main structure, which automatically cleans the toilet device after a pet defecates, particularly, after urination; a sub-structure; and a water container, which are formed and coupled into modular units so as to be slim and compact, wherein cleaning can be carried out by only the main structure without the sub-structure.