The beam structures that commonly exist in mechanical machineries are often impacted by vibration, the location of which was difficult to detect. A quantitative diagnostic method for rubbing location detection in a beam structure is thus proposed. The relationship between the high order harmonic components of the responses of the impacting beam was deduced based on the harmonic balance theorem. Harmonic components of the response difference between the fault and pre-fault system combined modal of beam structure were used to detect the impacting locations. Numerical simulations and experiments on the cantilever beam and complex beam structure show that the rubbing fault location was accurately detected, and the experiments that changed the damping matrix show that the method was rather robust. The advantage of this method is that the impacting location can be diagnosed with responses of only two nodes, and plenty of prior data was not needed, so this method was easy to apply in online diagnoses.