Osteoporosis (OP) is a systemic bone disease with a series of clinical symptoms. The use of screening biomarkers in OP management is therefore of clinical significance, especially in the era of precision medicine and intelligent healthcare. MicroRNAs (miRNAs) are small, non-coding RNAs with the potential to regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs may serve as biomarkers for OP prediction and prevention. However, few studies have emphasized the role of miRNAs in systems-level pathogenesis during OP development. In this article, literature-reported OP miRNAs were manually collected and analyzed based on a systems biology paradigm. Functional enrichment studies were performed to decode the underlying mechanisms of miRNAs in OP etiology and therapeutics in three-dimensional space, i.e., integrated miRNA-gene-pathway analysis. In particular, interactions between miRNAs and three well-known OP pathways, i.e., estrogenendocrine, WNT/β-catenin signaling, and RANKL/RANK/OPG, were systematically investigated, and the effects of non-genetic factors on personalized OP prevention and therapy were discussed. This article is a comprehensive review of OP miRNAs, and bridges the gap between an understanding of OP pathogenesis and clinical translation.