In the past decade, nanopores have been developed extensively for various potential applications, and their performance greatly depends on the surface properties of the nanopores. Atomic layer deposition (ALD) is a new technology for depositing thin films, which has been rapidly developed from a niche technology to an established method. ALD films can cover the surface in confined regions even in nano scale conformally, thus it is proved to be a powerful tool to modify the surface of the synthetic nanopores and also to fabricate complex nanopores. This review gives a brief introduction on nanopore synthesis and ALD fundamental knowledge, then focuses on the various aspects of synthetic nanopores processing by ALD and their applications, including single-molecule sensing, nanofluidic devices, nanostructure fabrication and other applications.