The molecular mechanism for the microgravity‐induced decrease in bone formation remains unclear and there is a lack of effective specific preventative therapies. We recently reported that primary cilia of osteoblasts became shorter and even disappeared when the cells were exposed to random positioning machine (RPM)‐simulated microgravity and that the microgravity‐induced loss of osteogenic potential of osteoblasts could be attenuated when the resorption of primary cilia was prevented by treatment with 0.1 μM cytochalasin D. In the current study, it was further found that the loss of the osteogenic capacity of rat calvarial osteoblasts (ROBs) was associated with the inhibition of the BMP‐2/Smad1/5/8 signalling pathway, of which most of the signalling proteins including BMP‐2, BMPRII, Smad1/5/8 and p‐Smad1/5/8 were found localized to primary cilia. Accompanying the resorption of primary cilia following the cells being exposed to simulated microgravity, the expression levels of these signalling proteins were reduced significantly. Furthermore, the expression of miRNA‐129‐3p, a microRNA previously reported to control cilium biogenesis, was found to be reduced quickly and changed in a similar tendency with the length of primary cilia. Moreover, overexpression of miRNA‐129‐3p in ROBs significantly attenuated microgravity‐induced inhibition of BMP‐2 signalling and loss of osteogenic differentiation and mineralization. These results indicated the important role of miRNA‐129‐3p in microgravity‐induced resorption of primary cilia of osteoblasts and the potential of replenishing the miRNA‐129‐3p as an effective countermeasure against microgravity‐induced loss of primary cilia and impairment of osteoblast function.