As one of the most important parameters in structural health monitoring, structural frequency has many advantages, such as convenient to be measured, high precision, and insensitive to noise. In addition, frequency-change-ratio based method had been validated to have the ability to identify the damage occurrence and location. However, building a precise enough finite elemental model (FEM) for the test structure is still a huge challenge for this frequency-change-ratio based damage detection technique. In order to overcome this disadvantage and extend the application for frequencies in structural health monitoring area, a novel method was developed in this paper by combining the cross-model cross-mode (CMCM) model updating algorithm with the frequency-change-ratio based method. At first, assuming the physical parameters, including the element mass and stiffness, of the test structure had been known with a certain value, then an initial to-be-updated model with these assumed parameters was constructed according to the typical mass and stiffness distribution characteristic of shear buildings. After that, this to-be-updated model was updated using CMCM algorithm by combining with the measured frequencies of the actual structure when no damage was introduced. Thus, this updated model was regarded as a representation of the FEM model of actual structure, because their modal information were almost the same. Finally, based on this updated model, the frequency-change-ratio based method can be further proceed to realize the damage detection and localization. In order to verify the effectiveness of the developed method, a four-level shear building was numerically simulated and two actual shear structures, including a three-level shear model and an eight-story frame, were experimentally test in laboratory, and all the test results demonstrate that the developed method can identify the structural damage occurrence and location effectively, even only very limited modal frequencies of the test structure were provided.