Pectin is a promising nano-carrier. The degree of methyl esterification (DM) influences the physiochemical properties of pectin. However, the effect of DM on the encapsulation capacity of pectin remains unclear. In this work, low methyl-esterified pectin (LMP) and high methyl-esterified pectin (HMP) were prepared. The molecular weight, rheological properties of these pectins with various DM levels were determined. Then icaritin/pectin micelles (IPMs) were prepared using HMP and LMP. Notably, higher loading capacities (18.75–20.12 %) were observed in HMP-IPMs compared to LMP-IPMs (15.72–16.64 %). Furthermore, LMP-IPMs demonstrated a DM-dependent reduction in particle sizes, ranging from 449 to 527 nm. In contrast, the particle sizes of HMP-IPMs varied between 342 and 566 nm, with smaller particle sizes observed in HMP-IPMs at higher DM levels. A significant positive correlation was found between DM and the formation of IPMs, including encapsulation efficiency, loading capacity, Zeta potential, and polydispersity index. Alkali de-esterification showed a weak impact on the pectin structure. Hydroxyl groups like 7-OH and 5-OH of icaritin might be involved in the formation of IPMs. The hydrogen-bond interactions between pectin and icaritin could be enhanced as DM increased.