Understanding the changing mechanism of phosphorus concentration in lakes is the precondition of strategic decision for lake restoration. Based on the 70 years (1949-2020) phosphorus concentration monitoring data at Lake Taihu, a large shallow lake, it is found that the phosphorus concentration was highly fluctuated temporally and spatially, owing to both human pollution and natural limnological changes. Phosphorus concentrations was largely different both in the relatively clean 1950 and in the relatively polluted recent 30 years. Heavy rain storm discharge plenty of external phosphorus into the lake, causing large spatial difference of water phosphorus concentration. Strong wind causing lots of phosphorus released from lake sediment, causing large temporal fluctuation of phosphorus concentration. And algal bloom materials re- distribution by wind driving also bring about large uncertainty of phosphorus concentrations. In the recent 20 years, pollution abatement projects have significantly changed the spatial-temporal change of phosphorus concentration in Lake Taihu. Zero Action of water pollution control in Taihu catchment since 1998, water resource diversion engineering since 2007, and the bloom situation aggravate since 2017 have significantly influenced the fluctuation intensity, spatial distribution and mean value of phosphorus in Lake Taihu. However, phosphorus concentrations in the whole Lake Taihu still keep high level even plenty of pollution treatment investigation. Its reasons are owing to both external loading factors, such as largely increase of construction land use ratios, population increases, and crop planting structure change in farmlands, and internal loading factors, such as submerged vegetation degradations, hydrological structure changes, and algal bloom aggravates under climatic change. The seventy years variation characteristic of phosphorus concentration in Lake Taihu should provide lessons for large shallow lakes management. Relatively large fluctuation of phosphorus concentration in lake water is the nature of large shallow lakes. Decision-maker should consider the natural characteristic when they formulate the protection target of large shallow lakes. External loading abatement should give priority, such as land use adjustment in Lake Taihu basin and deeply phosphorus removal in tail-water of urban sewage treatment plants. At the same time, internal loading control measures, such as submerged vegetation restoration and top-down food-web control of algal biomass by bio-manipulation of fishery should be undertaken to make sure the highly fluctuation of phosphorus being largely controlled.