Methylmalonic acidemia (MMA) is a metabolic disorder, which is caused by a deficiency of the mitochondrial enzyme methylmalonyl-CoA mutase. MMA diagnosis is dependent on the method of gas chromatography-mass spectrometry, which is expensive, complicated, and time consuming. Currently, microRNAs (miRNAs) have gained considerable interest for its function as a novel class of non-invasive and sensitive biomarkers for the diagnosis of diseases. However, there has been no related report regarding its role in MMA. Our study first detected differentially expressed microRNAs in MMA and found that the expression of miR-9-1 was significantly down-regulated and changed sensitively after VitB12 treatment. Furthermore, we confirmed that miR-9-1 was able to suppress neuronal apoptosis induced by methylmalonate. Taken together, our results suggested that miR-9-1 may act as a potential biomarker for the diagnosis and monitoring of changes in MMA and provide new insights into the pathogenesis of MMA.