For the multi-layer and multi-pass welding process of the heavy plate, the hydrogen diffusion behavior was numerically simulated to study the effect of solid-state phase transition (SSPT) on the hydrogen diffusion in the thickness direction, and the influence of the residual stress-induced diffusion after SSPT. The calculation results were compared with the experimental results. The comparison shows that the distribution of hydrogen concentration in the direction of thickness was in good agreement. The position with the most severe cold cracking sensitivity was located at a 20–30 mm depth from the top surface in this article. After welding, the hydrogen concentration in this position was kept at a high level for a long time under the effect of the size-constraint effect of the heavy plate and the existence of welding residual stress gradient. In addition, the SSPT reduced the residual stress level of weld metal (WM) significantly, increased that of the heat affected zone (HAZ), and the hydrogen was redistributed under the influence of stress. In the process of phase transformation, the parameters of hydrogen diffusion property of the material changed dramatically in a short time, the hydrogen diffusion coefficient increased in order of magnitude, and the solubility decreased in order of magnitude. This directly led to the upward diffusion of hydrogen in WM, and produced a self-gathering effect. For a welded joint of heavy plate, the self-gathering effect between passes was effective in the short-range and ineffective in the long-range.