Herb-induced liver injury (HILI) is a growing clinical and economic problem worldwide. However, the underlying mechanism of HILI remains largely unknown, which hinders the prevention and treatment of this disease. Recently evidence supports that microRNAs (miRNAs) in circulating exosomes and cells play an important role in the pathology of liver diseases. Thus, using Fructus Meliae Toosendan (FMT) as an example of hepatoxic herbal medicine, the aim of this study was to reveal the mechanisms of FMT-induced liver injury (FILI) through integrated analysis of serum exosomal miRNAs and liver miRNAs profiles on FMT ethyl acetate extract (FMT for short)-exposed mice. Two dosages of FMT (20 and 40 g/kg) were involved in this study, while only high-dose exposure induced obvious liver injury in mice. Pathway analysis of 209 differentially expressed miRNAs (DEMs) in serum exosomes between high-dose FMT and control groups exhibited that FILI might be regulated by apoptosis-related pathways, such as p53 signaling, PI3K/Akt signaling, and PTEN signaling. Integrated analysis of the mRNA targets of serum exosomal DEMs and liver DEMs of high-dose FMT group showed that autophagy was significantly enriched as one of the top canonical pathways in FILI. Hepatocyte apoptosis was then proved by TUNEL assay in the liver tissue of high-dose FMT-treated mice. Moreover, in vivo validation studies suggested that the protein expression levels of PTEN, p-AKT, p53, and BAX were indeed regulated in the mouse liver after high-dose FMT administration, indicating hepatocyte apoptosis may be mediated by these three pathways mentioned above. Intriguingly, PINK1/Parkin-mediated mitophagy was activated in high-dose FMT-treated mouse liver and the protective effect of autophagy in FILI was validated in vitro with an autophagic flux inhibitor. In addition, serum exosomal miR-222, the most downregulated miRNAs between low- and high-dose FMT treatments, might be an important event in the hepatocyte apoptosis by regulating PTEN and PPP2R2A. In conclusion, integrated analysis of microRNA profiles in mouse serum exosomes and liver cells provides insights into the hepatotoxicity mechanisms of FMT and discloses the protective role of autophagy in FILI, suggesting this method could contribute to deeply understand the mechanism of HILI and activation of autophagy may be a potentially therapeutic strategy for FILI even HILI.