Strong deep-current variabilities with periods of 8–25, 16–40, and 30–80 days observed in the northern South China Sea (NSCS) are interpreted as topographic Rossby waves (TRWs) based on the moored observations from July 25, 2017 to August 13, 2018. The TRWs present significantly spatial distribution in the frequency and intensity, which are largely controlled by the mesoscale perturbations in the upper layer. Longer period (30–80-day) TRWs observed to the west of the Dongsha Islands were excited by locally enhanced perturbations with the periods of 30–80 days in the upper ocean. The bottom currents in the periods of 8–25 days observed on the slope of the northeastern South China Sea (NESCS) were influenced by upper-layer mesoscale perturbations on their northeastern side through TRW propagation in the deep ocean in addition to local processes. In the Luzon Strait, deep currents with the periods of 16–40 days were associated with locally strong perturbations in the upper layer. The distribution of the bottom current variability was closely related to the spatial variability of the upper-layer fluctuations. The 8-25-day bandpass-filtered surface eddy kinetic energy (EKE) was overall maximal in the Luzon Strait and weakened westward to the east side of the Dongsha Islands, which explained why TRWs with the periods of 8–25 days were more energetic in the Luzon Strait. The surface fluctuations with the periods of 30–80 days were dominant in the west of the Dongsha Islands, and triggered the strong TRWs with the frequency band.