Uncertainty is introduced in modal parameter due to measurement noise. Uncertainties of modal parameter identification can be described by its statistical characteristics. Variance calculation is illustrated here for the complex modal indictor function identification method based on matrix sensitivity analysis and Kronecker algebra. The emphasis is put on calculating the covariance of enhanced frequency response functions and poles. Finally, both simulated case of a five degrees of freedom system and measurement case of a T-shaped structure are used to demonstrate the accuracy and practicability of the derived expressions.