Halloysite nanotubes (HNTs) have attracted much attention as delivery carriers for various drugs, but the loading of one such drug, quercetin, on HNTs has been investigated only rarely and usually involved cyclic vacuum pumping. The main objective of the present study was to develop a novel carrier system based on HNTs for quercetin delivery without a vacuum process and to investigate the effect of chemical modification of HNTs on the loading and release of quercetin. For this purpose, comparative studies of five chemical modification reagents (sodium lauroamphoacetate, cocoamidopropyl betaine, 1-hydroxyethyl 2-nonyl imidazoline betaine, triethanolamine, and dipicolinic acid) functionalized on HNTs were investigated for quercetin loading and in vitro release. Characterization of raw halloysite, modified halloysite, and quercetin-loaded halloysite were done by X-ray diffraction (XRD), Fourier-transform infrared spectrometry (FTIR), thermogravimetric analysis (TGA), and transmission electron microscopy (TEM). The results indicated that chemical modification could improve the interactions between HNTs and quercetin. After chemical modification, quercetin was anchored to both the inner and outer surfaces of HNTs by electrostatic attraction, hydrogen bonding, and van der Waals forces. Sodium lauroamphoacetate-modified HNTs were given the highest loading of 1.96 wt.% among the five reagents. Cocamidopropyl betaine-modified HNTs exhibited the best sustained-release profile with only 29.07% for initial burst release and 480 h of consecutive release. Carboxyl groups of the modification reagent improved the loading capacity of quercetin. Amide groups prolonged drug release due to the strong affinity between amine and phenolic hydroxyl groups of quercetin. The release of quercetin from the cocamidopropyl betaine-modified HNTs fitted a first-order kinetics model well. The present study suggested that cocamidopropyl betaine-modified HNTs offer promise as vehicles for delivery of quercetin and for extending the application of quercetin.