The double-deck vibrating flip-flow screen (DDVFFS) resolves the limitation of the traditional single-deck vibrating flip-flow screen, which cannot perform multi-granularity screening. The nonlinear characteristics of the springs in the DDVFFS lead to issues of unstable vibration and significant deviations between the operational and design amplitudes. Consequently, a dynamic equation incorporating cubic nonlinear stiffness is formulated. These equations are initially expressed in physical coordinates and subsequently transformed into modal coordinates for analyzing the system’s nonlinear vibration characteristics under resonance using the multi-scale method. The study then explores the impact of system parameters on this nonlinear behavior. Increasing damping or reducing harmonic forces proves effective in mitigating multiple solutions and vibration jumps. The operational frequency is chosen within the distant single-valued resonance region to minimize the influence of nonlinear stiffness, ensuring stable operation of the DDVFFS. The calculated amplitudes are as follows: the main frame shows an amplitude of 7 mm, whereas the upper and lower floating frames display amplitudes of 9.4 mm and 5.6 mm, respectively. A 180° phase difference between the main frame and the upper or lower frames facilitates deck stretching and slackening.