In order to solve the damage identification problem of engineering structures such as transmission tower with uncertain factor disturbance, a cloud reasoning algorithm based on associated mode is presented. Firstly, residual force equation is established and damage identification principle based on residual force vector is analyzed. Then, a cloud reasoning algorithm based on residual force is proposed. Numerical characteristics of cloud model are given, front cloud generator and rear cloud generator are analyzed, qualitative rules based on gray cloud model are proposed, and corresponding cloud reasoning system is composed by using cloud rules. Finally, given the drawback that residual force is susceptible to uncertain factors such as measurement noise, a cloud reasoning algorithm based on associated mode is further presented to enhance the identification accuracy and reliability. A transmission tower structure is applied to damage identification. The simulation results indicate that the cloud reasoning algorithm based on associated mode can well identify structural damage, and the identification results of the proposed algorithm are obviously superior to those of residual force vector method and the cloud reasoning algorithm based on residual force.