A method of manufacturing a nanochannel-array and a method of fabricating a nanodot using the nanochannel-array are provided. The nanochannel-array manufacturing method includes: performing first anodizing to form a first alumina layer having a channel array formed by a plurality of cavities on an aluminum substrate; etching the first alumina layer to a predetermined depth and forming a plurality of concave portions on the aluminum substrate, wherein each concave portion corresponds to the bottom of each channel of the first alumina layer; and performing second anodizing to form a second alumina layer having an array of a plurality of channels corresponding to the plurality of concave portions on the aluminum substrate. The array manufacturing method makes it possible to obtain finely ordered cavities and form nanoscale dots using the cavities.