From the principle of independent component analysis (ICA) and the uncertainty of amplitude, order, and number of source signals, this paper expounds the root reasons for modal energy uncertainty, identified order uncertainty, and modal missing in output-only modal analysis based on ICA methods. Aiming at the problem of lack of comparison and evaluation of different ICA algorithms for output-only modal analysis, this paper studies the different objective functions and optimization methods of ICA for output-only modal parameter identification. Simulation results on simply supported beam verify the effectiveness, robustness, and convergence rate of five different ICA algorithms for output-only modal parameters identification and show that maximization negentropy with quasi-Newton iterative of ICA method is more suitable for modal parameter identification.