Due to abundant low-frequency components of long-period ground motions (LPGMs), long-period structures, such as high-rise buildings, are susceptible to severe damage. Dual systems are widely used in high-rise and super high-rise buildings. Ensuring the cooperative work of dual systems is the key to realizing multiple seismic fortification lines and reasonable structural failure modes under severe earthquakes. However, the existing research on the influence of long-period ground motions on high-rise and super high-rise structures mainly focuses on the overall structural response. The influence of long-period ground motions on the cooperative performance of dual systems and its internal mechanism remains to be further studied. In view of this, firstly, the effects of ground motion frequency components on the cooperative performance of RC frame-shear wall structures were analyzed based on the empirical mode decomposition (EMD). Then, the simplified dynamics analysis model of RC frame-shear wall structure under harmonic vibration excitation was established, and the influence mechanism of LPGMs on cooperative working performance of RC frame-shear wall structures was discussed. The results showed that due to the low-frequency characteristics, LPGMs have a much more influence on the structure with a longer period, and the ratio of frame shear to base shear under LPGMs is much more than that under ordinary ground motions; the influence of ground motion frequency components on structural cooperative work is related to the component period and the structural period; when the excitation period is close to 0.6 times of the structural period, the ratio of frame shear to base shear exhibits a resonance-like phenomena, and its resonance peak could reach about 3 times of the stable value; the influence of the frequency characteristic of the excitation on the cooperative work should be considered during the seismic design of the frame-shear wall structures under long-period ground motions.