Mesoporous silica films consisting of highly ordered and vertically aligned nanochannels (abbreviated as VMSFs) have received considerable attention because of their high surface area, long-range order, thermal and mechanical stability, controllable pore size and more importantly good molecular accessibility for rapid mass transport. These characteristics are ideal for electroanalytical chemistry and separation science. In this review, we firstly present briefly the strategies for the synthesis of VMSFs on the electrode surface, mainly the electrochemically assisted self-assembly and Stöber-solution growth approaches, as well as the surface modification of channel walls with diverse terminal groups for various functionalities. In the next section, recent progress on the applications of VMSFs in electroanalytical chemistry and sensing is summarized, in terms of the spatial confinement and permselective effects (size, charge and lipophilicity selectivity of the mesochannels). We then present the preparation and application of perforated free-standing VMSFs for fast and precise molecular sieving/separation. The review ends with an outlook and perspective on the future applications of VMSFs.