Dinoflagellates demonstrate a variety of vertical migration patterns that presumably give them a competitive advantage when nutrients are depleted in the surface layer of stratified waters. In this study, a simple quota-based model was used to examine the relationships between the vertical migration pattern and internal nutritional status, and to assess how external environmental conditions, such as mixing layer depth (MLD) and internal waves, can influence these relationships. Dinoflagellates may form subsurface aggregations or conduct vertical migration (diel or non-diel) in response to their internal nutrient quota, but within a limited physiological parameter space. The model was implemented in a 1D (vertical) domain using an individual-based modeling approach, tracking the change in nutrient quota and the trajectory of many individual cells in a water column. The model shows that dinoflagellate cells might change from one vertical migration pattern to another when the external environmental conditions change. Using the average net growth rate as an index of fitness, 2 migration strategies, photo-/geotaxis vs. quota-based migration, were assessed with regard to MLD and internal wave regime. It was found that dinoflagellates might choose different migration strategies under different mixing/stratification regimes. In addition, under the same environmental conditions, different species might display unique vertical migration patterns due to inherent physiological differences. This study reveals the sensitivity of dinoflagellate vertical migration to biological and physical factors and offers possible explanations for the various vertical distributions and migration patterns observed in the field.