Phytoplankton physiologies are dynamic and have sensitive responses to the ambient environment. In this paper, we examine photosynthetic physiologies of phytoplankton communities with Phyto-PAM in the eastern equatorial Indian Ocean during the spring inter-monsoon. Environmental parameters were measured to investigate the coupling between phytoplankton photosynthetic physiologies and their habitats. During the cruise, the water column was highly stratified. The mixed layer extended to about 75 m and was characterized by high temperature (>28°C) and low nutrient level. The Fv/Fm values and chlorophyll a (Chl a) concentrations were lower at the surface, as consequences of nutrient depletion and photo-inhibition. Subsurface Chl a maximum (SCM) occurred between 75 and 100 m, and had the highest Fv/Fm values. The formation of SCM was a balance between nutrient availability and light limitation. The SCM may contribute significantly to pelagic food web and primary production in the water column. Phytoplankton in different layers encountered different light, trophic and hydrographic dynamics and evolved distinct photosynthetic characteristics. Despite of co-limitation of nutrient limitation and photo-inhibition, phytoplankton in the surface layer showed their acclimation to high irradiance, had lower light utilization efficiencies (α: 0.061±0.032) and could exploit a wide range of light irradiance. Whereas, phytoplankton in the SCM layers presented the highest light utilization efficiencies (α: 0.146±0.48), which guaranteed higher photosynthetic capacities under low light level. These results provide insights into phytoplankton photo-adaption strategies in this less explored region.