Bone nonunion caused by bacterial infection accounts for bone fractures, bone trauma and bone transplantation surgeries. Severe consequences include delayed unions and amputation and result in functional limitations, work disability, and poor quality of life. However, the mechanism of bone nonunion remains unknown. In this study, we aimed to screen the miRNA biomarkers of bacterial bone infection and investigated whether miRNAs regulate the osteoblasts and thus contribute to bone nonunion. We established a miRNA-mRNA network based on high-throughput RNA sequencing to compare the model rabbits infected with Staphylococcus aureus with the control rabbits. After validation experiments, miRNA-331-3p and fibroblast growth factor 23 (FGF23) were found to be inversely correlated with the pathways of osteoblast mineralization and pathology of infected bone nonunion. In in vitro experiments, miRNA-331-3p was downregulated and FGF23 was upregulated in lipopolysaccharide (LPS)-induced mouse calvarial osteoblasts. Further studies of the mechanism showed that mutated of putative miRNA-331-3p can bind to FGF23 3′-untranslated region sites. MiRNA-331-3p acted as an osteoblast mineralization promoter by directly targeting FGF23. Downregulation of miRNA-331-3p led to inhibition of osteoblast mineralization by regulating the DKK1/β-catenin mediated signaling. Thus, we established an improved animal model and identified new bone-related biomarkers in the infected bone nonunion. The miRNA-331-3p biomarker was demonstrated to regulate osteoblast mineralization by targeting FGF23. The novel mechanism can be used as potential diagnostic biomarkers and therapeutic targets in the infected bone nonunion and other inflammatory bone disorders.