Icaritin is a bioactive compound with low stability and poor bioavailability. Development of icaritin/polysaccharide complex can improve them. However, the structure information of this complex remains unclear. In this study, icaritin-loaded pectin micelles (IPMs) with high encapsulation efficiency (>93%) and loading capacity (>18%) were constructed. NMR spectra revealed that A ring of icaritin was involved in direct interaction with pectin. A new intermolecular hydrogen bond between 7-OH of icaritin and hydroxyl in pectin was formed, which could further influence the chemical shifts of 5-OH and 6-H. Cryo-scanning electron microscope image of IPMs showed a dense and layered network filled with twining fibers. Compared to free icaritin, the bioaccessibility of icaritin in IPMs was improved by 28-fold. The particle size, Zeta potential and stability of IPMs were determined. The results showed that IPMs had smaller particles (594–667 nm) than pectin alone (740 nm). IPMs remained stable at pH 2.0–6.0.