In recent years, eutrophication has become a serious problem in the Changjiang estuary and adjacent regions and has led to more frequent occurrences of harmful algal blooms (HABs). Prorocentrum donghaiense and Skeletonema costatum are two common HAB species in the East China Sea. Because of the differences in the niches of these two species, bloom events caused by P. donghaiense usually occur after those caused by S. costatum. Many studies have been conducted to clarify the relationship between these two species but the mechanisms controlling the bloom succession from S. costatum to P. donghaiense remains unresolved. To understand the mechanisms underlying HABs in the Changjiang estuary, two zero-dimensional box models were constructed using the physiological features of P. donghaiense and S. costatum. These models were used as examples of the application of modeling to research into algal competition and succession. We chose the phytoplankton component of the Eco3M (Ecological, Mechanistic and Modular Modelling) system to build our model. The main biological processes of P. donghaiense and S. costatum were considered in our simulation. These included growth, nutrient uptake, chlorophyll synthesis, and other processes. The complete equations also considered S. costatum dynamics, dissolved inorganic nutrients, dissolved organic carbon, and particulate matter. In Eco3M, algal growth depends on a combination of photosynthesis, respiration, and mortality in relation to temperature, salinity, irradiance, and dissolved inorganic nutrient concentrations. The biomass of species is expressed as carbon and the environmental impacts on species growth are parameterized by estimating their influences on growth rate. A global respiration rate is derived by considering, for each active process, its respiratory cost per process unit (specific unit cost) and the rate at which this process takes place. The gross uptake rate depends on ambient nutrient concentrations and enzymatic activity at the cell membrane. Particulate matter is generated as a result of the death of phytoplankton. Laboratory experiments using mono-algal cultures with different initial densities were conducted to calibrate the models. Most of the other parameter values were average estimates derived from experiments in the literature. The models were used to simulate monospecific growth experiments at different N/P ratios and to determine levels of competition between the two algae (bi-algal cultures). Comparison of the simulation with the laboratory findings demonstrated that these models could accurately represent the growth of the two algae and their uptake of nutrients in monospecific experiments with different N/P ratios. In the experiments with bi-algal cultures, the final densities of S. costatum exceeded those of P. donghaiense in all cultures and nutrient uptake by S. costatum was the main cause of PO₄ depletion. The simulated data were consistent with the laboratory findings, indicating that the model could predict the effects of nutrient competition between the two algae. Because the model was limited to interactions concerned with nutrient competition, it did not simulate the rapid decrease in the density of P. donghaiense cells observed in the laboratory. This model could serve as a component of a general environmental model for the region of the East China Sea. In the future, the model will be adjusted to examine further scenarios that consider other nutrients, other algal species, and algal predators.