Environmental and operational variables are inevitable concerns by researchers and engineers when implementing the damage detection algorithm in practical projects, because the change of structural behavior could be masked by the conditions in a large extent. Thus, reliable damage detection methods should have a virtue of immunity from environmental and operational variables. In this paper, the pair cointegration method was presented as a novel way to remove the effect of environmental variables. At the beginning, the concept and procedure of this approach were introduced, and then the theoretical formulation and numerical simulations were put forward to illustrate the feasibility. The jump exceeding the control limit in the residual indicates the occurrence of damage, while the direction and magnitude imply the most potential damage location. In addition, the simulation results show that the proposed method has strong ability to resist the noise.