In this paper, we report a study of the low-lying states of deformed 21Ne within the framework of the quantum-number projected generator coordinate method (PGCM), starting from a chiral two-nucleon-plus-three-nucleon (NN+3N) interaction. The wave functions of states are constructed as a linear combination of a set of axially deformed Hartree–Fock–Bogliubov (HFB) wave functions with different quadrupole deformations. These HFB wave functions are projected onto different angular momenta and the correct neutron and proton numbers for 21Ne. The results of the calculations based on the effective Hamiltonians derived by normal-ordering the 3N interaction with respect to three different reference states, including the quantum-number projected HFB wave functions for 20Ne, 22Ne, and an ensemble of them with equal weights, are compared. This study serves as a key step towards ab initio calculations of odd-mass deformed nuclei with the in-medium GCM.