Single-walled carbon nanotubes (SWCNTs) have the potential to revolutionize nanoscale electronics and power sources; however, their low purity and high separation cost limit their use in practical applications. Here we present a supramolecular chemistry-based one-pot, less expensive, scalable, and highly efficient separation of a solubilizer/adsorbent-free pure semiconducting SWCNT (sc-SWCNT) using flavin/isoalloxazine analogues with different substituents. On the basis of both experimental and computational simulations (DFT study), we have revealed the molecular requirements of the solubilizers as well as provided a possible mechanism for such a highly efficient selective sc-SWCNT separation. The present sorting method is very simple (one-pot) and gives a promising sc-SWCNT separation methodology. Thus, the study provides insight for the molecular design of an sc-SWCNT solubilizer with a high (n,m)-chiral selectivity, which benefits many areas including semiconducting nanoelectronics, thermoelectric, bio and energy materials, and devices using solubilizer-free very pure sc-SWCNTs.