The open-sea ecosystem is usually divided into several subsystems: epipelagic, mesopelagic, bathypelagic, abyssopelagic zones, etc. Many findings indicated that plankton communities showed significant temporal and spatial variations in the epipelagic zone, mainly because of the variations of light, temperature, ice, nutrient supplements, etc. However, in the mesopelagic and deeper zones, more stable physical and chemical environments with increased depths resulted in weaker temporal and spatial variations of ecosystems than those in the epipelagic zone. Besides, our knowledge about the general patterns of the temporal and spatial variation of deep-sea ecosystems has been seriously restricted by limited investigation technology and funding. With the development of marine science and the implementation of marine strategies, the focus of our marine research has evolved from the limited neritic area to coordination of neritic, marginal, and open seas. However, China's scientific contribution to deep-sea ecology, especially zooplankton ecology of the mesopelagic, bathypelagic, and abyssopelagic zones, has been more limited than that of the neritic zone in the past several decades. The present paper provides an overview of the current progress of deep-sea zooplankton ecology, including the vertical distribution and variation of deep-sea zooplankton communities, interspecific relationships, and niche differentiation, and their roles in carbon deposition and the biogeochemical cycle, etc. Furthermore, the investigation technology of deep-sea zooplankton ecology has developed remarkably in recent years.