Traditional multi-reference impact testing (MRIT) has the merit to identify not only the structural modal parameters but also structural flexibility, however, it requires a large number of sensors mounted on the entire structure which leads to expensive experiment cost. A new mobile impact testing method is proposed in this article for a more efficient flexibility identification of bridges. In the proposed method, the structure under investigation is subdivided into smaller substructures which are tested independently. Then the experimental data collected from all sub-structures are integrated by taking the interface measurement as a reference for flexibility identification of the entire structure. The new impact testing method only requires limited instrumentation, thus it can be performed rapidly and efficiently. Especially, the signal processing procedure developed in the proposed method is able to identify the full flexibility matrix of the entire structure from the sparse FRF matrices of the sub-structures. Numerical and experimental examples studied successfully verify the effectiveness of the proposed method by comparing its results with those from the traditional MRIT method for structural flexibility identification and deflection prediction.