In recent years, increasing attention has focused on seismic performance of long-span continuous rigid-frame bridges (CRFBs) under near-fault earthquake excitations. To investigate the characteristics of near-fault seismic response of CRFBs and evaluate the effectiveness of a hybrid seismic control system (HSCS), this study establishes 22 uncontrolled models and 22 controlled models varying in span and pier height. A comprehensive seismic evaluation method based on a fuzzy logic control (FLC) algorithm is proposed. Transverse whiplash and spatial torsion effects of the uncontrolled and controlled models are analyzed comparatively. Control performance of HSCS is evaluated and parametric study is conducted to investigate the effect of friction, damping, and ground motion on seismic response of HSCS-controlled CRFB. The results indicate that, in practical applications, the transverse whiplash and spatial torsion effects of CRFBs should be considered, particularly in multi-span CRFBs with unequal-height piers. The span and pier height have significant impact on these two effects and the corresponding girder end displacement, girder base, and pier bottom moment. Controlled bridges exhibit lower levels of these responses compared to uncontrolled bridges, and the displacement and bending moment are markedly reduced at a high control ratio of 0.4. Parametric analysis results show that the HSCS provides excellent seismic control performance for near-fault CRFBs when the optimum parameter values are used. This study may provide a useful reference for the seismic design and performance improvement of near-fault CRFBs.