Aleurolyphus ovatus Troupeau is one of the most predominant species of the Acaridae family worldwide. Recent reports have demonstrated that the accumulation of lead in stored grains and dietary items exceeds the required standards. However, the molecular mechanism of heavy metal stress on mites has not been reported. To understand the mechanism underlying the heavy metal response of A. ovatus, comparative transcriptome analysis was performed in this study using an Illumina high throughput mRNA sequencing (RNA-seq) platform. A. ovatus was fed on artificial diets containing two different concentrations of lead, namely, a low concentration of 12.5 mg/kg (LAO) and a high concentration of 100 mg/kg (HAO), while the mites in the control (NAO) group were not exposed to lead. A total of 44,362 unigenes, with an average length of 1547 bp, were identified. Of these, 996 unigenes were successfully annotated in seven functional databases. The number of differentially expressed genes (DEGs) in A. ovatus under different lead concentrations was compared. In NAO versus LAO group, including 310 up-regulated and 1580 down-regulated DEGs. In NAO versus HAO group, including 3928 up-regulated and 1761 down-regulated DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that detoxification enzyme genes were significantly expressed in pathways, such as cytochrome P450 foreign body metabolism, glutathione metabolism and drug metabolism-cytochrome pathway. The results of gene annotation and quantitative real-time PCR showed that high concentration of lead significantly stimulated the expression of metabolic detoxification enzyme genes such as glutathione S transferase (GST) and superoxide dismutase (SOD), while low concentration inhibited their expression. This study will provide a basis for the molecular mechanism of A. ovatus in response to heavy metal lead stimulation in stored grain.