The diversity of phytoplankton is fundamental to the health of aquatic ecosystems. Those commonly used diversity indices (e.g., Shannon-weiner diversity index, etc.) were assumed that a uniform distribution was the optimal status of phytoplankton taxa in aquatic system during the assessment of these indices. We discovered that the relative abundance of phytoplankton within an aquatic ecosystem can be fitted with exponential distribution, suggesting that the exponential distribution was the intrinsic and inherent distribution of phytoplankton communities. Through mathematical derivation, taxa capacity (N), competition coefficient (k), critical relative abundance of extinction (a), degree of monopoly, and the residual sum of squares of the phytoplankton community can be obtained to provide a greater insight into phytoplankton diversity. Our results highlight a new methodology based on the above indices has been developed to provide a better insight into the phytoplankton community diversity. It will also help to evaluate the aquatic system ecological health.