In the ship-hull design phase, the distance of a misalignment of a cruciform welded joint is enlarged, by up to 100 mm for example, until its effect is thought to be minimized. To control tolerance, we used a technique to estimate the coefficient of the misalignment effect: the ratio of the stress with misalignment to stress without misalignment. Current methods, created using the two-dimensional (2D) misalignment model and focusing on small misalignments, cannot be applied in the design phase. Misalignment models are needed, as there have been no studies of these joints and it is impractical to do finite element (FE) analysis in each case. We propose an estimation method of the coefficient of misalignment effect in three dimensions (3D). First, we created a new equation to estimate the coefficient in 2D. The equation accommodates larger misalignments. Second, we found the membrane component of a misaligned member stress is reduced as a 3D effect and the coefficient converges given a certain misalignment value. Third, a modified equation taking the effect into account indicates the coefficient in 3D.