Decidualization of human endometrial stromal cells (hESCs) is important for the maintenance of a successful pregnancy. Histone deacetylase 4 (HDAC4) was reported to be involved in the dysfunction of decidua-derived mesenchymal stem cells. However, the role of HDAC4 underlying decidualization of hESCs remains unclear. We intended to explore the function and molecular mechanism of HDAC4 in hESCs. In vitro expansion of hESCs using a serum-free medium was used to confirm the characteristics of hESCs. Gene expression in hESCs was evaluated by reverse transcription-quantitative polymerase chain reaction. CCK-8 assay, TUNEL staining, flow cytometry analysis, and Western blot analysis were performed to test the effects of HDAC4 and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) on hESCs. RNA pull-down and luciferase reporter assays were performed to validate the relationship between genes. In this study, the characteristics of hESCs were sustained in serum-free medium during a process of propagation. HDAC4 knockdown suppressed hESCs viability and promoted hESCs apoptosis. HDAC4 was targeted by miR-498-3p in hESCs. MALAT1 bound with miR-498-3p in hESCs. HDAC4 expression was positively regulated by MALAT1 and negatively regulated by miR-498-3p in hESCs. HDAC4 upregulation countervailed the effects of MALAT1 silencing on hESCs proliferation, apoptosis, and decidualization of hESCs. Overall, MALAT1 facilitated the decidualization of hESCs via binding with miR-498-3p and upregulating HDAC4, which might provide a new direction for the maintenance of a successful pregnancy.