This article shows a new strategy for the fabrication of nanofluidics based on nanoscale gaps in nanopillar arrays. Silicon nanopillar arrays are prepared in a designed position by combining conventional photolithography with colloidal lithography. The nanogaps between the pillars are used as nanochannels for the connection of two polydimethylsiloxane-based microchannels in microfluidics. The gap between neighbouring nanopillars can be accurately controlled by changing the size of initial colloidal spheres and by an etching process, which further determines the dimensions of the nanochannels. At a low ionic strength, the surface charge-governed ion transportation shows that the nanochannels possess the same electrokinetic properties as typical nanofluidics. Benefiting from the advantage of photolithography, large-area nanochannel arrays can be prepared in a parallel manner. Due to the perm-selectivity of the nanochannels, the nanofluidic chips can be used to preconcentrate low concentration samples. The large-area ordered nanostructures preserve their high-throughput property and large surface-to-volume ratio, which shows their great potential in the development of nanofluidics and their applications, such as in the separation of small molecules, energy conversion, etc.