The harmonic balance method (HBM) is an efficient frequency-domain approach to computing periodically unsteady flows. The basic principle of this method is to decompose the flow variables into a Fourier series, and transform the unsteady flow into several steady problems coupled by a spectral time-derivative operator, from which the whole time history of a complete unsteady periodic flow can be reconstructed. In the present work, we investigate the ability of the HBM to be used for modeling the periodic unsteady vortex shedding behind a bluff body at low Reynolds numbers via solving the unsteady incompressible Navier-Stokes equations. For the periodic problem where the time period T of the unsteadiness is unknown, a variable-time-period method based on residual gradients is used to compute the exact time period iteratively starting from an initial guess T₀. By simulating the two-dimensional laminar flows over a circular cylinder and a square cylinder, the accuracy and efficiency of the HBM are investigated and the effects of different parameters on the final results are analyzed. Comparisons with the results of fixed-time-period HBM using a constant time period are also implemented. Three practical methods of optimization are used to iterate the time period, and the values of accuracy and efficiency of different methods are compared with each other. The results show that the HBM can accurately capture the complex nonlinear flow field physics with only three harmonics. The Strouhal frequency and mean drag coefficient each as a function of the Reynolds number agree well with existing experimental and computational data. For both test cases, the computational efficiency of HBM is higher than that from the traditional time-domain method. For the square cylinder test case, the HBM offers speedup rate up to nearly 18 times. The real time period of vortex shedding can be predicted by the gradient based variable-time-period method, and the final result is insensitive to search step λ. The calculation result is sensitive to the initial T₀, and when such a variable is greater than a certain value, the result will converge to an approximate integer multiple of the real one. Therefore, it deserves further exploration on how to specify this initial condition. The shedding time periods computed by different optimization methods are converged to the same value. The computational efficiency from the FR conjugate gradient method and that from Newton method are both equivalent to that from the steepest descent method with the maximum search step λ = 100. Avoiding prescribing parameters such as the search step λ, the Newton method possesses higher application value in engineering calculation than the other two schemes.