Endohedral nitrogen fullerenes have been proposed as building blocks for quantum information processing due to their long spin coherence time. However, addressability of the individual electron spin levels in such a multiplet system of S-4(3/2) has never been achieved because of the molecular isotropy and transition degeneracy among the Zeeman levels. Herein, by molecular engineering, we lifted the degeneracy by zero-field splitting effects and made the multiple transitions addressable by a liquid-crystal-assisted method. The endohedral nitrogen fullerene derivatives with rigid addends of spiro structure and large aspect ratios of regioselective bis-addition improve the ordering of the spin ensemble. These samples empower endohedral-fullerene-based qudits, in which the transitions between the 4 electron spin levels were respectively addressed and coherently manipulated. The quantum geometric phase manipulation, which has long been proposed for the advantages in error tolerance and gating speed, was implemented in a pure electron spin system using molecules for the first time.