Flexibility plays an important role in bridge load-carrying capacity assessment. The flexibility of bridges has been extracted from the measured data of numerical impact testing and in laboratory experiments. Recently, substructuring impact testing has been increasingly investigated and developed because it avoids deploying sensors throughout bridges while obtaining the same results as full-structure testing. However, most substructuring testing methods require overlapping transition areas between the divided substructures, thereby affecting the operability and efficiency of the test. This study proposes a novel substructuring flexibility integration method that uses limited instruments to sequentially test different substructures subdivided from the whole girder bridge structure without requiring the overlapping reference points of adjacent substructures. Using the basis that the structural mode shapes satisfy the orthogonality and mode node theorem, the parameters of each substructure can be efficiently integrated and the entire flexibility matrix can be identified from the sparse flexibility matrices of the substructures. Case studies using experimental data from a cantilever beam and a continuous girder bridge are considered to verify the availability and effectiveness of the proposed method.