The shipbuilding industry employs numerous cutting and joining processes to build the ship and offshore structure. Welding, as the primary joining process, inherently causes distortion and accounts for most of the major geometrical variation in the intermediate products (IPs), thus adversarially affecting the downstream assembly processes. Because of the welding process, the variation analysis of compliant assemblies in shipbuilding is clearly different from that of the automobile and aerospace industries, where the distortion during the joining process is negligible. This paper proposes a variation simulation model including the effects of joining process distortion for ships and offshore structures. The proposed model extends the concepts of the sources of variation and the method of influence coefficient (MIC) for a compliant mechanical assembly to include the welding distortions. The proposed model utilizes welding distortion patterns and a transformation matrix to efficiently model the deformation due to the joining process. Also the welding distortions are represented as stochastic values due to its randomness. The model is verified by case study simulation and by a comparison with welding experimental results.