Increasingly complex civil structures lead to enormous consume of computational resource in response reconstruction, and common closely spaced modes (CSMs) also impair reconstruction performance. An improved approach incorporating substructural condensation and modal-group superposition was presented. To extrapolate the desired response more efficiently, multiple manageable substructures divided from the whole finite element model are condensed and assembled into a super-element model with less DOFs. By selectively retaining physical measured DOFs during the condensation process, reconstruction response could be directly performed on the condensed model. Aiming to deal with the situation of CSMs, the defined modal-group responses (MGRs) are extracted from dynamic measurement through empirical mode decomposition (EMD), from which corresponding MGRs at inaccessible locations are extrapolated based on the condensed model. Finally, all MGRs are superposed to form the desired response. Numerical and experimental cases were performed to demonstrate the efficiency and accuracy of this approach. Effects of substructural division, measurement noise and measurement locations on reconstruction were studied in detail.