Hyperplasia of mammary glands (HMG) is also termed mammary dysplasia. In China, the number of patients suffering from breast hyperplasia is increasing annually. MicroRNAs (miRNAs; length, 19–24 nucleotides), a group of small endogenous non-coding RNAs, post-transcriptionally regulate gene expression via RNA interference and gene silencing pathways. The cause of disease of HMG because remains unclear. Thus, the aim of the present study was to establish comprehensive profile of drug treatments following at different time intervals on rat models of differentially expressed miRNAs, using miRNA microarray data. After scanning the chip, 13 up-regulated and 20 down-regulated miRNAs were identified. MiR-31 and miR-30 exhibited different expression levels between rats exhibiting mammary gland hyperplasia treated with or without Jiedu Capsule water solution once a day for 4 weeks, and the two demonstrated a strong association with HMG and breast cancer. Therefore, the functions of these miRNAs may provide the basis for further investigation of HMG.