Objective To detect the level of serum long noncoding RNA HOXBAS3 (LncRNA HOXBAS3) in patients with myelodysplastic syndrome (MDS) and to explore its relationship with MDS. Methods From March 2017 to December 2019, a total of 74 MDS patients in our hospital were treated as MDS group. The 74 MDS patients were divided into lowrisk group, middlerisk group Ⅰ, middlerisk group Ⅱ and highrisk group according to the international prognostic score system (IPSS). According to WHO classification, the patients were divided into refractory anemia (RA) group, refractory cytopenia multiple dysplasia (RCMD) group, refractory anemia with excess blasts type Ⅰ (RAEBⅠ) group and refractory anemia with excess blasts type Ⅱ (RAEBⅡ) group. 68 healthy people were selected as the control group. The level of serum LncRNA HOXBAS3 was detected by realtime fluorescent quantitative PCR (qRTPCR). The relationship between the expression of HOXBAS3 mRNA and IPSS score was analyzed. The relationship between the expression of HOXBAS3 mRNA in serum and WHO grading was analyzed. The diagnostic value of HOXBAS3 mRNA level in serum for MDS was analyzed. Results The expression level of HOXBAS3 mRNA in MDS group was significantly higher than that in control group (P＜0.05). The expression level of serum HOXBAS3 mRNA in high risk group was significantly higher than that in low risk group, medium risk group Ⅰ and medium risk groupⅡ (P＜0.05). The expression level of HOXBAS3 mRNA in RAEBⅡ group was significantly higher than that in RA group and RCMD group (P＜0.05). The expression of HOXBAS3 mRNA was positively correlated with IPSS score and WHO grade (r=0550, 0597, P＜0.05). Conclusion The expression of serum LncRNA HOXBAS3 may have a predictive effect on the occurrence of MDS and may be of great significance for the evaluation of the development of MDS, and provide some reference for the early intervention of MDS.