This paper proposes an efficient beam-shell modeling technique for the free vibration analysis of a T-joint thin-walled beam structure. Except a small portion of a T-joint which is modeled by shell elements, the structure is modeled by thin-walled beam elements that can describe warping and distortion. In order to match the shell and thin-walled beam elements at the interface of the dissimilar elements, a technique based on a pseudo inverse matrix is formulated. This paper also examines the role of the thin-walled element taking into account the distortion and warping deformation degrees of freedom in predicting accurately the dynamic characteristics of a T-joint thin-walled structure.