The Bosten Lake is the largest inland freshwater lake of China, in which water level and salinity fluctuate due to the imbalance between inflows and outflows under climate change and anthropogenic activities. This paper employed system dynamics as an effective methodology to grasp the regulation rules for sustainable freshwater management of the Bosten Lake. Results show the following. (1) Changing of lake water salinity is not only affected by the salinity of water entering and leaving, but is mostly a result of water exchange rate (WER) and the lake level fluctuation. (2) According to the estimated regime of lake level regulations, it is attested that surface water inflow must be larger than outflow about 10.6 × 108 m3 every year. Thus, the Bosten Lake can keep its normal water level. (3) A nonlinear equation was fitted between WER and average salinity of the Bosten Lake. This equation quantifies that when WER equals, or is larger than, 7, the Bosten Lake can be kept as a freshwater lake at all times.