Precisely controlled spatial distributions of artificial light-harvesting systems in aqueous media are of significant importance for mimicking natural light-harvesting systems; however, they are often restrained by the solubility and the aggregation-caused quenching effect of the hydrophobic chromophores. Herein, we report one highly efficient artificial light-harvesting system based on peptoid nanotubes that mimic the hierarchical cylindrical structure of natural systems. The high crystallinity of these nanotubes enabled the organization of arrays of donor chromophores with precisely controlled spatial distributions, favoring an efficient Förster resonance energy transfer (FRET) process in aqueous media. This FRET system exhibits an extremely high efficiency of 98.6% with a fluorescence quantum yield of 40% and an antenna effect of 29.9. We further demonstrated the use of this artificial light-harvesting system for quantifying miR-210 within cancer cells. The fluorescence intensity ratio of donor to acceptor is linearly related to the concentration of intercellular miR-210 in the range of 3.3–156 copies/cell. Such high sensitivity in intracellular detection of miR-210 using this artificial light-harvesting system offers a great opportunity and pathways for biological imaging and detection, and for the further creation of microRNA (miRNA) toolbox for quantitative epigenetics and personalized medicine.