Phosphorus is an essential element for life and an important limiting factor for food production. The biogeochemical cycles of phosphorus not only regulate marine primary production, but also has an impact on the global climate system; it also determines the formation and distribution of phosphate resources and affects the continuity of life on earth. The current theory of “earth system science” integrates the subsystems of atmosphere, hydrosphere, lithosphere (crust and upper mantle) and biosphere, providing a broader view for studying the global phosphorus cycles. Based on the existing research and combined with the theory of “earth system science”, the following important understandings of the biogeochemical cycles of phosphorus has been obtained: The evolution of phosphorus in geological history determines the current cycle pattern of phosphorus on a global scale (terrestrial ecosystems and marine ecosystems); Human industrial and agricultural activities, as an important geological agent, has changed the biogeochemical cycles of phosphorus, resulted in resource crisis of phosphate depletion and environmental problem of eutrophication of water bodies; The key to solve the resource crisis problem of phosphorus shortage and environmental pollution problem of phosphorus surplus lies in regulating the biogeochemical cycle process that cause these problems.