Extracorporeal shockwave therapy (ESWT) has shown chondroprotective effects on the initiation of the osteoarthritis (OA) changes of the rat knee. This study evaluated 69 significant expressed profiles of microRNA (miRNA) in the articular cartilage and subchondral bone after ESWT. There were 118 target genes identified for miRNAs of interest in articular cartilage and 214 target genes in subchondral bone by next generation sequencing (NGS). In principal component analysis (PCA), the relationships of miRNA expression in bone and cartilage were improved after ESWT. Global functional annotation showed that predicted targets were involved in cartilage development, inflammatory and immune response, ion binding, angiogenesis, cell adhesion, cell cycle, transcription and translation, gene expression, NTP binding, signal transduction, collagen fibril organization, apoptotic process, chondrocyte differentiation, cell differentiation, bone development as well as cell proliferation. The miRNAs profile and the target genes were comprehensively surveyed and compared in articular cartilage and subchondral bone of early OA knee before and after ESWT. Our study represents the direct assessment to date of miRNA expression profiling in early OA articular cartilage and subchondral bone. The results provide insights that could contribute to the development of new biomarkers and therapeutic strategies for OA changes and the treatment with ESWT.