The generalized gradient approximation （GGA） based on density functional theory（DFT）is used to analyze the structure, bonding and magnetic properties of the transition metal atom doped endohedral fullerene Ni@C20H20. The geometric optimization shows that the Ni atoms situated at the three possible positions off the cage center are all drawn back to the cage center. The binding energy and the energy gap calculations tell us that the cage center is the most thermodynamically and dynamically stable site for the Ni atom. It is discovered from the bonding analysis that the interaction between Ni and the cage could be neglected and the Ni atom keeps its atomic character. The electronic and magnetic properties reveal that the Ni atom with 2μB magnetic moments has no magnetism, while the cage with no magnetism still has no magnetic moment, mainly due to the zero electron transference between the Ni and the cage.