The ion diffusion in an open nanofluidic system is studied by using an array of nanochannels. The mechanism of the ion diffusion was described through electrowetting-based nanofluidics. An ion diffusion experiment was conducted to validate the theoretical study of the relationship between the diffusion length and the ionic concentration using sodium chloride and phosphate buffer solutions. Shadow edge lithography was utilized to fabricate an array of open nanochannels, which allowed for a direct observation of the molecular diffusion through optical microscopy. The open channel configuration was then applied to stretching -DNA molecules in the nanochannels. The stretched length was measured by fluorescence microscopy. The presented nanofluidic device can be applied to the single-molecule study, which can benefit nanoengineered medicine and biology.