A data processing apparatus and a data processing method thereof are provided. The data processing apparatus includes a register and a processor electrically connected to the register. The register is stored with a plurality of data. The plurality of data each includes a first sub-datum and a second sub-datum. The plurality of first sub-data corresponds to a first column and the plurality of second sub-data corresponds to a second column. The processor compresses the first sub-data by a first compression algorithm according to a first characteristic of the plurality of first sub-data and compresses the second sub-data by a second compression algorithm according to a second characteristic of the plurality of second sub-data.