This study was aimed to investigate the cytogenetic changes of MDS cell line (MUTZ-1) with chromosome 5q deletion. R-banding analysis was used to identify chromosome aberrations in MDS cell line and Vysis Spectra Vysion M-FISH was used to further characterize chromosomal complex karyotype. The results indicated that M-FISH exhibited obvious chromosomal aberrations with high frequency including translocation, insertion, breakage and rearrangement, deletion and increasement of chromosome number, the complex karyotype of MUTZ-1 was shown as 50, xx, der (1) t (1;2), ins (1;14), +der (2) t(2;19), der (3) t (3;5), der (3) (3::5::22), 5q-, der (6) t (3;6), der (7) (18::7::17), +8, +der (9) t (1;9), der (10) t (1;10), +11, +12, der (?13) (10::13::5::8), der (14) t (8;14), der (14) t (14, 15), der (15) t (15;21) x 2, +17, +18, -21, -22. It is concluded that M-FISH analysis revealed obvious changes in complex karyotype of MDS cell line MUTZ-1, and the M-FISH technique can increase accuracy of detection for chromosomal complex karyotype, and help diagnosis and prognostic evaluation of MDS.