The Humboldt Current System (HCS) supports the largest pelagic fisheries in the world, and is also strongly affected by climate forces in the Eastern Boundary Currents System. In this study, the sea conditions of the HCS and status of its fishery were summarized, then the effects of marine environment and climate changes on growth and reproduction, population structure and resource fluctuation of four representative fishery species, Peruvian anchovy (Engraulis ringens), Chilean jack mackerel (Trachurus murphyi), Pacific sardine (Sardinops melanosticta) and Jumbo flying squid (Dosidicus gigas) were further discussed. This study suggested that the species abundance and distribution of the above four pelagic economic species are strongly influenced by seasonal, interannual and interdecadal climate changes and oceanic conditions of the HCS. Furthermore, research on the Humboldt current ecosystem(HCES) under the influence of future climate change is expected to be highly dependent on high-capacity comprehensive ecosystem models, considering physical environment, biochemical reaction, nutritional structure and other factors. Based on the models and their evaluations, a thorough understanding of the variations of various kinds of population in the HCES will facilitate a more reasonable development and scientific management of the fishery resources within such system.