A keyhole-TIG welding method assisted with alternating axial magnetic field (MF) was proposed to obtain qualified cryogenic toughness joints. The results show that the MF can refine prior austenite grains and establish distinct Ni-rich grain boundaries. Furthermore, the electron back scatter diffraction data demonstrate that the martensite grains have also been refined, and there is a higher density high angle grain boundary (HAGB) in the MF-assisted joint than in the ordinary joint. Under the cryogenic (−196 °C) Charpy V-notch impact test, the MF-assisted joint express a 37 J absorbed energy, which is 300% higher than the 11.7 J of the ordinary joint. This extraordinary increasing in toughness results from the refinement of grains and high density distribution of HAGB, which act as obstacles to crack propagation in cleavage fracture and form small facets on the fracture surface. The MF-assisted welding method has been proven to obtain qualified 9Ni steel joints.