Missed abortion (MA) is a common disease in obstetrics and gynecology. More and more studies have focused on the relationship between miRNAs and pregnancy maintenance and its related diseases. The aim of this article is to explore the relationship between miRNA and MA. The expression of miR-98 were detected by in situ hybridization and real-time PCR. Cell proliferation, activity and migration were measured via Edu, MTT, and transwell assays. The target genes of miR-98 are identified by dual-luciferase activity assay. And the expression levels of target genes were determined by Western blot, real-time PCR and immunohistochemistry. miR-98 was significantly up-regulated in placental villi from over 35 years old MA patients compared with the age-matched normal pregnant women. Up-regulation of miR-98 suppressed the proliferation, activity and migration of the human trophoblast HTR-8/SVneo cell in vitro. miR-98 could bind to GDF6 and FAPP2 mRNA 3’-UTR and negatively regulate their expression. The downregulation of miR-98 promoted cell proliferation, then knockdown of GDF6 or FAPP2 inhibited miR-98-mediated cell proliferation. GDF6 and FAPP2 expression in the placental villi from MA patients were decreased compared to normal placental tissues. The expression of miR-98 in MA had an opposite relationship with the expression of GDF6 and FAPP2. Overexpression of miR-98 is associated with the occurrence of MA. miR-98 prevents proliferation, viability and migration of trophoblast cells partially through targeting GDF6 and FAPP2.