[Objective] Freak wave is a marine disaster characterized by extremely large wave height, strong nonlinearity, and high destructiveness. The results of wave superposition method for simulating freak waves are influenced by multiple parameters, and the sensitivity and interaction mechanisms of these factors require systematic investigation. [Methods] Based on a self-developed viscous-flow numerical wave tank, we conducted a numerical simulation on the generation of freak waves and their influencing factors. First, the reliability of the numerical model was verified against physical experimental data. Subsequently, the harmonic separation method was employed to examine the influence of wave group nonlinearity on wave surface deformation, focusing characteristics, and frequency spectrum structure. Through numerical experiments, the effects of key parameters—including spectral type, number of constituent waves, spectral bandwidth, spectral peak frequency, and water depth—were investigated. [Results] 1) During the generation of a freak wave, wave-wave nonlinear interactions caused energy to transfer from the primary frequency to both high and low frequencies, resulting in significant spectral broadening. Low-frequency free pseudo-harmonics propagated faster, leading to an actual wave height slightly larger than the theoretical value. High-frequency bound harmonics formed a tail wave, which had a minor influence on the shape of the main peak. 2) The spectral type significantly influenced the wave profile characteristics: the JONSWAP and P-M spectra, with concentrated energy, tended to generate freak waves with steep crests. The CWA spectrum produced gentle wave profiles; the CWS spectrum yielded the smallest focused amplitude. 3) The number of constituent waves affected the focusing recurrence period. An insufficient number could generate secondary focused waves. It was recommended to use 29 constituent waves to balance computational accuracy and efficiency. 4) Under finite water depth conditions, the focused amplitude reached its maximum when the spectral bandwidth was 0.7 Hz, indicating that the amplitude was co-modulated by the spectral bandwidth, water depth, and spectral peak frequency. 5) An increase in the spectral peak frequency enhanced nonlinearity, resulting in wave profile steepening. However, an excessively high frequency led to wave breaking, thereby reducing the amplitude. 6) Water depth influenced the wave profile by altering the dispersion characteristics. A greater water depth resulted in faster wave speed and a higher amplitude, whereas an excessively small water depth readily induced wave breaking. [Conclusion] The main innovations of this research include: establishing a high-precision viscous-flow numerical model capable of accurately simulating the evolution of nonlinear waves including breaking effects; employing the harmonic separation method to reveal the influence mechanism of wave group nonlinearity on wave surface structure and energy distribution; and clarifying the coupling effects of various factors under finite water depth conditions through multi-parameter sensitivity experiments. The findings of this study deepen the understanding of freak wave generation mechanisms, provide an important theoretical basis and parameter selection guidance for laboratory simulation of freak waves.