A cat litter box cleaning system designed to sieve waste clumps from cat litter is provided. The cat litter box cleaning system has multiple layers thereby providing multiple cleaning operations. The layers may consist of a sieving layer and a liner. The liner shields the sieving layer from the cat's claws and the sieving layer is used to remove the waste from the litter. Each sieving layer and liner releasably cooperates with layer securing fixtures. The layer securing fixtures releasably attach the layers to a base and prevent the cat from dislodging the sieves or liners. Access ports may be provided for removing the layers from the layer securing fixtures without having to come into contact with the cat litter. A method is provided where at least two cat litter box cleaning systems are utilized to ensure that fresh cat litter always forms the basis of the litter used.