Objective To investigate the effect of microgravity on MC3T3-E1 osteoblast differentiation. Methods The differential miRNA and mRNA expression profiling of MC3T3-E1 cells during exposure to microgravity were established by RNA transcriptome sequencing technology (RNA-seq). The RNA sequencing results were validated using quantitative real-time polymerase chain reaction (q-PCR). Bioinformatic analyses were applied for further study of these differentially expressed miRNAs and mRNAs. Results Compared with control (CON) group, A total of 1 912 coding transcripts and 160 miRNAs were detected along with osteogenic differentiation in simulated microgravity (SMG) group. Bioinformatic analysis revealed 10 core regulatory genes including 7 mRNAs and 3 miRNAs. Based on the analysis and verification, one miRNA, miR-9_6666-5p, was identified, which might play an important role in osteogenic differentiation process under microgravity. Conclusions The process of osteoblast differentiation was repressed under microgravity which might be related to the changed expression profile of miRNA/mRNA. The research findings can contribute to the better understanding of the molecular mechanisms of mRNA and miRNAs in osteogenic differentiation and bone formation under the microgravity condition.