The subject of this study was the complex structure of a wooden historic church, which consisted of several segments that differed in the material used, the structural system employed, and the degree of wear of the elements. Particularly examined were the multi-branched columns located at the junction of different segments. The main objective of the analyses was to determine the degree of bonding of the column branches and the effect of this bonding on the operation of the entire structure. To evaluate the degree of bonding of the column branches, it was proposed to use experimental modal analysis. Based on the results of the experiment, it was found that the column branches are connected, but their cooperation is limited. Several computational models of the analyzed structure were also created, differing, for example, in the degree of bonding of the column branches. The effect of bonding the column branches on the values of stresses in the nave columns and on the values of extreme wind-induced displacements was studied.