The column base connections exhibit unpredictable semi-rigid behavior due to the fact that their basic components including base plate, anchor bolts and concrete foundation, are made from different material types and transmitting acting forces through unilateral multi-body contact. To address this need, this study seeks to develop a quite general base connection modelling capable of accurately representing material and geometrical nonlinear behavior of base connection, and its implementation in a time domain finite element seismic analysis through an incremental-iterative procedure is presented. A representative problem of cable-stayed bridges tower subjected to strong ground motion is analyzed. The maximum bearing stress on the concrete foundation as well as the tension force per anchor bolt that necessary to design the anchorage system is computed. The seismic responses of the tower structure with physical model of the base connection are compared to those of rigid base model. The semi-rigid connection model yields more economical solutions than rigid base model.