Emerging technologies have significant implications in establishing competitive advantages and are characterized by continuous rapid development. Efficient benchmarking is more and more important in the development of emerging technologies. Similar input level and importance are two necessary criteria need to be considered for emerging technology`s benchmarking. In this study, we proposed a sequential use of self-organizing map(SOM), data envelopment analysis(DEA) and analytical hierarchy process(AHP) method for the stepwise benchmarking of emerging technology. The proposed method uses two-level SOM to cluster the emerging technologies with similar required input levels together, then, in each cluster, uses DEA-BCC model to evaluate the efficiencies of the emerging technologies and do tier analysis to form tiers. On each tier, AHP rating method is used to calculate each emerging technology`s importance priority. The optimal benchmarking path of each cluster is established by connecting the emerging technologies with the highest importance priority. In order to validate the proposed method, we apply it to a case of biotechnology. The result shows the proposed method can overcome difficulties in benchmarking, select suitable benchmarking targets and make the benchmarking process more efficient and reasonable.