The interstory drift-based scaling procedure (IDS) developed recently by the authors for plane frames under single component horizontal ground motions, has been extended to three-dimensional structures possessing torsional coupling under bi-axial ground motions which are represented by their geometric mean spectrum. The ground motion-scaling factor is defined as the ratio of average interstory drift along building height under target spectrum versus that under the associated ground motion spectrum. Hence, scaling is conditioned on structural response, which is in turn a function of seismic intensity. IDS for 3D systems is applied to 20-story and 3-story concrete space frames with mass and stiffness eccentricity, respectively. Accuracy and efficiency of the IDS procedure is assessed under a set of near-fault strong motion pairs from large magnitude events. The results revealed that the proposed procedure is accurate and noticeably more efficient as compared to conventional procedures suggested in seismic codes and in literature. Further, the intensity measure employed in the IDS procedure is proved as a good predictor of fundamental demand measures (maximum interstory drift ratio and maximum plastic rotations) obtained from nonlinear dynamic analyses under individual ground motion pairs. Hence, employing the intensity measure of IDS for ground motion scaling in intensity-based evaluation of structures is proposed for reliable estimation of structural performance under code-prescribed seismic hazard.