Hydrogen plays a significant role in the microstructure evolution and macroscopic deformation of materials, causing swelling and surface blistering to reduce service life. In the present work, the atomistic mechanisms of hydrogen bubble nucleation in vanadium were studied by first-principles calculations. The interstitial hydrogen atoms cannot form significant bound states with other hydrogen atoms in bulk vanadium, which explains the absence of hydrogen self-clustering from the experiments. To find the possible origin of hydrogen bubble in vanadium, we explored the minimum sizes of a vacancy cluster in vanadium for the formation of hydrogen molecule. We show that a freestanding hydrogen molecule can form and remain relatively stable in the center of a 54-hydrogen atom saturated 27-vacancy cluster.