Our previous study showed that bone marrow mesenchymal stem cell derived exosomes (BMSC-Exos) suppress high phosphorus (Pi)-induced calcification of vascular smooth muscle cells (VSMCs). However, the mechanism had remained unclear. This study aimed to investigate the mechanism by which BMSC-Exos inhibit vascular calcification (VC). We found that BMSC-Exos reduced high Pi-induced Runx2, osteocalcin and BMP2 expression and inhibited the calcium deposition. Gene expression of human VSMCs stimulated by Pi or Pi plus BMSC-Exos (Pi + Exo) was systematically examined by microarray technology. NONHSAT 084969.2 and transcription factor p65 expression was significantly lower in the Pi + Exo group compared with the Pi group. This finding indicated that NONHSAT 084969.2 and the nuclear factor-κB pathway might play an important role in VC inhibition by BMSC-Exos. By silencing NONHSAT 084969.2 with small interfering RNA, Runx2, BMP2, and osteocalcin expression was decreased significantly. The calcified nodule content and alkaline phosphatase activity were reduced after NONHSAT 084969.2 inhibition and p65, p50, and IκB kinase-α expression was decreased significantly. These results indicated that BMSC-Exos inhibited Pi-induced transdifferentiation and calcification of VSMCs by regulating the NONHSAT 084969.2/nuclear factor-κB axis.