A method of manufacturing a nanoparticle chain is disclosed. The method comprises the steps of: providing a single-stranded circular primer with a determined length, and amplifying the single-stranded circular primer into single-stranded DNA nanotemplate by an isothermal nucleotide amplification reaction such that an end of the single-stranded DNA nanotemplate is fixed to a surface of a substrate; and adding a single-stranded DNA probe conjugated with nanoparticle at one end of which, and attaching the single-stranded DNA probe to the corresponding sequence on the single-stranded DNA nanotemplate to form a nanoparticles chain. The method of manufacturing a nanoparticle chain further comprises providing a fluid, and the flowing direction of the fluid controls the aligning direction of the nanoparticle chain. Wherein, the inter-nanoparticle distance of the nanoparticle chain can be adjusted by adjusting a reaction temperature or adding the single-stranded DNA probe without conjugating with nanoparticles.