Recently, the Revised International Prognostic Scoring System (IPSS-R) has been developed for assessing the prognosis of primary myelodysplastic syndromes (MDS) and has shown satisfactory outcomes for prognostic stratification. In this new system, cytogenetics remains the key stratification parameter and karyotypic abnormalities are classified into five prognostic subgroups with more uncommon cytogenetic subsets. Using this system, we analyzed the cytogenetic features of 532 adult Chinese patients with primary MDS and assessed the impacts of the IPSS-R cytogenetic categories on the prognosis of the disease without intensive treatment. Here, we show that the cytogenetic features of this cohort of Chinese patients are different from those of previously reported Western populations with MDS. In our Chinese patients, trisomy 8 was the most common anomaly, and the incidence rate of del(5q) was lower than that in the Western population. In the IPSS-R cytogenetic subgroups, the median survival was 59 months for the good risk, 36 months for the intermediate risk, 15 months for the poor risk and 10 months for the very poor risk subgroups (p < 0.001). In conclusion, the IPSS-R can effectively stratify the prognosis of MDS based on cytogenetics, but the prognostic significances of some karyotypes in the IPSS-R still need to be confirmed by larger multicenter cooperative studies.