This study was purposed to compare and analyze the relationship between the abnormality of chromosome karyotypes and diagnosis, prognosis of MDS and AML patients, as well as to explore the characteristics of chromosome prognostic stratification in MDS and AML patients of different ages. The cytogenetic karyotype analysis was performed in 134 cases of MDS and 123 cases of AML by using bone marrow short-term culture and R-banding technique. The results indicated that the detected rates of chromosome abnormal karyotypes in MDS and AML patients were 41% and 61% respectively. The abnormal karyotype analysis of MDS and AML group showed that the abnormal karyotype in MDS group displayed number abnormality as the dominate (mainly the +8), while the abnormal karyotype in AML group displayed structure abnormality as the dominant [mainly, t(15;17) and t(8;21)]. The detected abnormal karyotype are mainly for the +8 which has ambiguous correlation with FAB subtype; the detection rates of complex karyotype abnormalities, favourable prognosis karyotype as well as poor prognosis karyotype in the MDS group obviously higher than that of AML group. Among patients with MDS transformed into AML, 12 cases had chromosome abnormal karyotype. There were 3 cases of chromosome abnormal karyotype in AML group which were transformed by MDS. The analysis of age stratification between two groups showed that the detected rate of abnormal karyotype was enhanced with the increase of age in MDS group, and detected rate in ≥ 60 years old group was obviously higher than that in patients with ≤ 30 age group.The detected rate of complex karyotype abnormalities in three age groups of MDS did not show statistical difference; the detected rate of abnormal karyotype in AML group decreased with the increase of age, the detected rate in ≤ 30 years old group was obviously higher than that in ≥ 60 age group,while the detection rate of complex karyotype abnormalities showed that the detected rate in patients ≥ 60 years old group was obviously higher than that in patients with ≤ 30 years old group; Analysis of karyotype prognosis revealed that the detected rate of poor prognosis karyotype increased along with the age growth both in MDS and AML groups, and detected rate in ≥ 60 years old group was obviously higher than that in ≤ 30 years old group; while analysis of favourable prognosis karyotype in MDS and AML group showed that the detected rate in ≤ 30 years old group was obviously higher than that in ≥ 60 years old group. It is concluded that the patients with MDS and AML have higher chromosomal abnormalities,which have important reference value for the diagnosis, treatment and prognosis, meanwhile, the analysis of chromosome karyotype provides an important basis for prognostic stratification.